int
main (int argc, char **argv)
{
sc_MPI_Comm mpicomm;
int mpiret;
int mpisize, mpirank;
p4est_t *p4est;
p4est_connectivity_t *conn;
sc_array_t *points_per_dim, *cone_sizes, *cones,
*cone_orientations, *coords,
*children, *parents, *childids, *leaves, *remotes;
p4est_locidx_t first_local_quad = -1;
/* initialize MPI */
mpiret = sc_MPI_Init (&argc, &argv);
SC_CHECK_MPI (mpiret);
mpicomm = sc_MPI_COMM_WORLD;
mpiret = sc_MPI_Comm_size (mpicomm, &mpisize);
SC_CHECK_MPI (mpiret);
mpiret = sc_MPI_Comm_rank (mpicomm, &mpirank);
SC_CHECK_MPI (mpiret);
sc_init (mpicomm, 1, 1, NULL, SC_LP_DEFAULT);
p4est_init (NULL, SC_LP_DEFAULT);
#ifndef P4_TO_P8
conn = p4est_connectivity_new_moebius ();
#else
conn = p8est_connectivity_new_rotcubes ();
#endif
p4est = p4est_new_ext (mpicomm, conn, 0, 1, 1, 0, NULL, NULL);
p4est_refine (p4est, 1, refine_fn, NULL);
p4est_balance (p4est, P4EST_CONNECT_FULL, NULL);
p4est_partition (p4est, 0, NULL);
points_per_dim = sc_array_new (sizeof (p4est_locidx_t));
cone_sizes = sc_array_new (sizeof (p4est_locidx_t));
cones = sc_array_new (sizeof (p4est_locidx_t));
cone_orientations = sc_array_new (sizeof (p4est_locidx_t));
coords = sc_array_new (3 * sizeof (double));
children = sc_array_new (sizeof (p4est_locidx_t));
parents = sc_array_new (sizeof (p4est_locidx_t));
childids = sc_array_new (sizeof (p4est_locidx_t));
leaves = sc_array_new (sizeof (p4est_locidx_t));
remotes = sc_array_new (2 * sizeof (p4est_locidx_t));
p4est_get_plex_data (p4est, P4EST_CONNECT_FULL, (mpisize > 1) ? 2 : 0,
&first_local_quad, points_per_dim, cone_sizes, cones,
cone_orientations, coords, children, parents, childids,
leaves, remotes);
#ifdef P4EST_WITH_PETSC
{
PetscErrorCode ierr;
DM plex, refTree;
PetscInt pStart, pEnd;
PetscSection parentSection;
PetscSF pointSF;
size_t zz, count;
locidx_to_PetscInt (points_per_dim);
locidx_to_PetscInt (cone_sizes);
locidx_to_PetscInt (cones);
locidx_to_PetscInt (cone_orientations);
coords_double_to_PetscScalar (coords);
locidx_to_PetscInt (children);
locidx_to_PetscInt (parents);
locidx_to_PetscInt (childids);
locidx_to_PetscInt (leaves);
locidx_pair_to_PetscSFNode (remotes);
P4EST_GLOBAL_PRODUCTION ("Begin PETSc routines\n");
ierr = PetscInitialize (&argc, &argv, 0, help);
CHKERRQ (ierr);
ierr = DMPlexCreate (mpicomm, &plex);
CHKERRQ (ierr);
ierr = DMSetDimension (plex, P4EST_DIM);
CHKERRQ (ierr);
ierr = DMSetCoordinateDim (plex, 3);
CHKERRQ (ierr);
ierr = DMPlexCreateFromDAG (plex, P4EST_DIM,
(PetscInt *) points_per_dim->array,
(PetscInt *) cone_sizes->array,
(PetscInt *) cones->array,
(PetscInt *) cone_orientations->array,
(PetscScalar *) coords->array);
CHKERRQ (ierr);
ierr = PetscSFCreate (mpicomm, &pointSF);
CHKERRQ (ierr);
ierr =
DMPlexCreateDefaultReferenceTree (mpicomm, P4EST_DIM, PETSC_FALSE,
&refTree);
CHKERRQ (ierr);
ierr = DMPlexSetReferenceTree (plex, refTree);
CHKERRQ (ierr);
ierr = DMDestroy (&refTree);
CHKERRQ (ierr);
ierr = PetscSectionCreate (mpicomm, &parentSection);
CHKERRQ (ierr);
ierr = DMPlexGetChart (plex, &pStart, &pEnd);
CHKERRQ (ierr);
ierr = PetscSectionSetChart (parentSection, pStart, pEnd);
CHKERRQ (ierr);
count = children->elem_count;
for (zz = 0; zz < count; zz++) {
PetscInt child =
*((PetscInt *) sc_array_index (children, zz));
ierr = PetscSectionSetDof (parentSection, child, 1);
CHKERRQ (ierr);
}
ierr = PetscSectionSetUp (parentSection);
CHKERRQ (ierr);
ierr =
DMPlexSetTree (plex, parentSection, (PetscInt *) parents->array,
(PetscInt *) childids->array);
CHKERRQ (ierr);
ierr = PetscSectionDestroy (&parentSection);
CHKERRQ (ierr);
ierr =
PetscSFSetGraph (pointSF, pEnd - pStart, (PetscInt) leaves->elem_count,
(PetscInt *) leaves->array, PETSC_COPY_VALUES,
(PetscSFNode *) remotes->array, PETSC_COPY_VALUES);
CHKERRQ (ierr);
ierr = DMViewFromOptions (plex, NULL, "-dm_view");
CHKERRQ (ierr);
/* TODO: test with rigid body modes as in plex ex3 */
ierr = DMDestroy (&plex);
CHKERRQ (ierr);
ierr = PetscFinalize ();
P4EST_GLOBAL_PRODUCTION ("End PETSc routines\n");
}
#endif
sc_array_destroy (points_per_dim);
sc_array_destroy (cone_sizes);
sc_array_destroy (cones);
sc_array_destroy (cone_orientations);
sc_array_destroy (coords);
sc_array_destroy (children);
sc_array_destroy (parents);
sc_array_destroy (childids);
sc_array_destroy (leaves);
sc_array_destroy (remotes);
p4est_destroy (p4est);
p4est_connectivity_destroy (conn);
sc_finalize ();
mpiret = sc_MPI_Finalize ();
SC_CHECK_MPI (mpiret);
return 0;
}
static PetscErrorCode DMPlexTSSetupGeometry(DM dm, PetscFV fvm, DMTS_Plex *dmplexts)
{
DM dmFace, dmCell;
DMLabel ghostLabel;
PetscSection sectionFace, sectionCell;
PetscSection coordSection;
Vec coordinates;
PetscReal minradius;
PetscScalar *fgeom, *cgeom;
PetscInt dim, cStart, cEnd, cEndInterior, c, fStart, fEnd, f;
PetscErrorCode ierr;
PetscFunctionBegin;
if (dmplexts->setupGeom) PetscFunctionReturn(0);
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
/* Make cell centroids and volumes */
ierr = DMClone(dm, &dmCell);CHKERRQ(ierr);
ierr = DMSetCoordinateSection(dmCell, coordSection);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dmCell, coordinates);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionCell);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionCell, c, sizeof(CellGeom)/sizeof(PetscScalar));CHKERRQ(ierr);}
ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dmCell, sectionCell);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr);
ierr = DMCreateLocalVector(dmCell, &dmplexts->cellgeom);CHKERRQ(ierr);
ierr = VecGetArray(dmplexts->cellgeom, &cgeom);CHKERRQ(ierr);
for (c = cStart; c < cEndInterior; ++c) {
CellGeom *cg;
ierr = DMPlexPointLocalRef(dmCell, c, cgeom, &cg);CHKERRQ(ierr);
ierr = PetscMemzero(cg, sizeof(*cg));CHKERRQ(ierr);
ierr = DMPlexComputeCellGeometryFVM(dmCell, c, &cg->volume, cg->centroid, NULL);CHKERRQ(ierr);
}
/* Compute face normals and minimum cell radius */
ierr = DMClone(dm, &dmFace);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionFace);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
ierr = PetscSectionSetChart(sectionFace, fStart, fEnd);CHKERRQ(ierr);
for (f = fStart; f < fEnd; ++f) {ierr = PetscSectionSetDof(sectionFace, f, sizeof(FaceGeom)/sizeof(PetscScalar));CHKERRQ(ierr);}
ierr = PetscSectionSetUp(sectionFace);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dmFace, sectionFace);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ionFace);CHKERRQ(ierr);
ierr = DMCreateLocalVector(dmFace, &dmplexts->facegeom);CHKERRQ(ierr);
ierr = VecGetArray(dmplexts->facegeom, &fgeom);CHKERRQ(ierr);
ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr);
minradius = PETSC_MAX_REAL;
for (f = fStart; f < fEnd; ++f) {
FaceGeom *fg;
PetscReal area;
PetscInt ghost, d;
ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
ierr = DMPlexPointLocalRef(dmFace, f, fgeom, &fg);CHKERRQ(ierr);
ierr = DMPlexComputeCellGeometryFVM(dm, f, &area, fg->centroid, fg->normal);CHKERRQ(ierr);
for (d = 0; d < dim; ++d) fg->normal[d] *= area;
/* Flip face orientation if necessary to match ordering in support, and Update minimum radius */
{
CellGeom *cL, *cR;
const PetscInt *cells;
PetscReal *lcentroid, *rcentroid;
PetscReal v[3];
ierr = DMPlexGetSupport(dm, f, &cells);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cells[0], cgeom, &cL);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cells[1], cgeom, &cR);CHKERRQ(ierr);
lcentroid = cells[0] >= cEndInterior ? fg->centroid : cL->centroid;
rcentroid = cells[1] >= cEndInterior ? fg->centroid : cR->centroid;
WaxpyD(dim, -1, lcentroid, rcentroid, v);
if (DotRealD(dim, fg->normal, v) < 0) {
for (d = 0; d < dim; ++d) fg->normal[d] = -fg->normal[d];
}
if (DotRealD(dim, fg->normal, v) <= 0) {
if (dim == 2) SETERRQ5(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed, normal (%g,%g) v (%g,%g)", f, (double) fg->normal[0], (double) fg->normal[1], (double) v[0], (double) v[1]);
if (dim == 3) SETERRQ7(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed, normal (%g,%g,%g) v (%g,%g,%g)", f, (double) fg->normal[0], (double) fg->normal[1], (double) fg->normal[2], (double) v[0], (double) v[1], (double) v[2]);
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed", f);
}
if (cells[0] < cEndInterior) {
WaxpyD(dim, -1, fg->centroid, cL->centroid, v);
minradius = PetscMin(minradius, NormD(dim, v));
}
if (cells[1] < cEndInterior) {
WaxpyD(dim, -1, fg->centroid, cR->centroid, v);
minradius = PetscMin(minradius, NormD(dim, v));
}
}
}
ierr = MPI_Allreduce(&minradius, &dmplexts->minradius, 1, MPIU_REAL, MPI_MIN, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr);
/* Compute centroids of ghost cells */
for (c = cEndInterior; c < cEnd; ++c) {
FaceGeom *fg;
const PetscInt *cone, *support;
PetscInt coneSize, supportSize, s;
ierr = DMPlexGetConeSize(dmCell, c, &coneSize);CHKERRQ(ierr);
if (coneSize != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Ghost cell %d has cone size %d != 1", c, coneSize);
ierr = DMPlexGetCone(dmCell, c, &cone);CHKERRQ(ierr);
ierr = DMPlexGetSupportSize(dmCell, cone[0], &supportSize);CHKERRQ(ierr);
if (supportSize != 2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %d has support size %d != 1", cone[0], supportSize);
ierr = DMPlexGetSupport(dmCell, cone[0], &support);CHKERRQ(ierr);
ierr = DMPlexPointLocalRef(dmFace, cone[0], fgeom, &fg);CHKERRQ(ierr);
for (s = 0; s < 2; ++s) {
/* Reflect ghost centroid across plane of face */
if (support[s] == c) {
const CellGeom *ci;
CellGeom *cg;
PetscReal c2f[3], a;
ierr = DMPlexPointLocalRead(dmCell, support[(s+1)%2], cgeom, &ci);CHKERRQ(ierr);
WaxpyD(dim, -1, ci->centroid, fg->centroid, c2f); /* cell to face centroid */
a = DotRealD(dim, c2f, fg->normal)/DotRealD(dim, fg->normal, fg->normal);
ierr = DMPlexPointLocalRef(dmCell, support[s], cgeom, &cg);CHKERRQ(ierr);
WaxpyD(dim, 2*a, fg->normal, ci->centroid, cg->centroid);
cg->volume = ci->volume;
}
}
}
ierr = VecRestoreArray(dmplexts->facegeom, &fgeom);CHKERRQ(ierr);
ierr = VecRestoreArray(dmplexts->cellgeom, &cgeom);CHKERRQ(ierr);
ierr = DMDestroy(&dmCell);CHKERRQ(ierr);
ierr = DMDestroy(&dmFace);CHKERRQ(ierr);
dmplexts->setupGeom = PETSC_TRUE;
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
DM dm;
PetscSection s;
Vec u;
AppCtx user;
PetscInt cells[3] = {2, 2, 2};
PetscInt size = 0, cStart, cEnd, cell, c, f, i, j;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
ierr = DMPlexCreateHexBoxMesh(PETSC_COMM_WORLD, user.dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &dm);CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
/* Create a section for SEM order k */
{
PetscInt *numDof, d;
ierr = PetscMalloc1(user.Nf*(user.dim+1), &numDof);CHKERRQ(ierr);
for (f = 0; f < user.Nf; ++f) {
for (d = 0; d <= user.dim; ++d) numDof[f*(user.dim+1)+d] = PetscPowInt(user.k[f]-1, d)*user.Nc[f];
size += PetscPowInt(user.k[f]+1, d)*user.Nc[f];
}
ierr = DMPlexCreateSection(dm, user.dim, user.Nf, user.Nc, numDof, 0, NULL, NULL, NULL, NULL, &s);CHKERRQ(ierr);
ierr = SetSymmetries(dm, s, &user);CHKERRQ(ierr);
ierr = PetscFree(numDof);CHKERRQ(ierr);
}
ierr = DMSetDefaultSection(dm, s);CHKERRQ(ierr);
/* Create spectral ordering and load in data */
ierr = DMPlexCreateSpectralClosurePermutation(dm, NULL);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &u);CHKERRQ(ierr);
switch (user.dim) {
case 2: ierr = LoadData2D(dm, 2, 2, size, u, &user);CHKERRQ(ierr);break;
case 3: ierr = LoadData3D(dm, 2, 2, 2, size, u, &user);CHKERRQ(ierr);break;
}
/* Remove ordering and check some values */
ierr = PetscSectionSetClosurePermutation(s, (PetscObject) dm, NULL);CHKERRQ(ierr);
switch (user.dim) {
case 2:
ierr = CheckPoint(dm, u, 0, &user);CHKERRQ(ierr);
ierr = CheckPoint(dm, u, 13, &user);CHKERRQ(ierr);
ierr = CheckPoint(dm, u, 15, &user);CHKERRQ(ierr);
ierr = CheckPoint(dm, u, 19, &user);CHKERRQ(ierr);
break;
case 3:
ierr = CheckPoint(dm, u, 0, &user);CHKERRQ(ierr);
ierr = CheckPoint(dm, u, 13, &user);CHKERRQ(ierr);
ierr = CheckPoint(dm, u, 15, &user);CHKERRQ(ierr);
ierr = CheckPoint(dm, u, 19, &user);CHKERRQ(ierr);
break;
}
/* Recreate spectral ordering and read out data */
ierr = DMPlexCreateSpectralClosurePermutation(dm, s);CHKERRQ(ierr);
switch (user.dim) {
case 2: ierr = ReadData2D(dm, u, &user);CHKERRQ(ierr);break;
case 3: ierr = ReadData3D(dm, u, &user);CHKERRQ(ierr);break;
}
ierr = DMRestoreLocalVector(dm, &u);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&s);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFree(user.Nc);CHKERRQ(ierr);
ierr = PetscFree(user.k);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/* This assumes that the DM has been cloned prior to the call */
PetscErrorCode DMCreateSubDM_Section_Private(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm)
{
PetscSection section, sectionGlobal;
PetscInt *subIndices;
PetscInt subSize = 0, subOff = 0, nF, f, pStart, pEnd, p;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!numFields) PetscFunctionReturn(0);
ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);
ierr = DMGetDefaultGlobalSection(dm, §ionGlobal);CHKERRQ(ierr);
if (!section) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default section for DM before splitting fields");
if (!sectionGlobal) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default global section for DM before splitting fields");
ierr = PetscSectionGetNumFields(section, &nF);CHKERRQ(ierr);
if (numFields > nF) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Number of requested fields %d greater than number of DM fields %d", numFields, nF);
if (is) {
ierr = PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt gdof;
ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr);
if (gdof > 0) {
for (f = 0; f < numFields; ++f) {
PetscInt fdof, fcdof;
ierr = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr);
ierr = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr);
subSize += fdof-fcdof;
}
}
}
ierr = PetscMalloc1(subSize, &subIndices);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt gdof, goff;
ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr);
if (gdof > 0) {
ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
for (f = 0; f < numFields; ++f) {
PetscInt fdof, fcdof, fc, f2, poff = 0;
/* Can get rid of this loop by storing field information in the global section */
for (f2 = 0; f2 < fields[f]; ++f2) {
ierr = PetscSectionGetFieldDof(section, p, f2, &fdof);CHKERRQ(ierr);
ierr = PetscSectionGetFieldConstraintDof(section, p, f2, &fcdof);CHKERRQ(ierr);
poff += fdof-fcdof;
}
ierr = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr);
ierr = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr);
for (fc = 0; fc < fdof-fcdof; ++fc, ++subOff) {
subIndices[subOff] = goff+poff+fc;
}
}
}
}
ierr = ISCreateGeneral(PetscObjectComm((PetscObject)dm), subSize, subIndices, PETSC_OWN_POINTER, is);CHKERRQ(ierr);
}
if (subdm) {
PetscSection subsection;
PetscBool haveNull = PETSC_FALSE;
PetscInt f, nf = 0;
ierr = PetscSectionCreateSubsection(section, numFields, fields, &subsection);CHKERRQ(ierr);
ierr = DMSetDefaultSection(*subdm, subsection);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&subsection);CHKERRQ(ierr);
for (f = 0; f < numFields; ++f) {
(*subdm)->nullspaceConstructors[f] = dm->nullspaceConstructors[fields[f]];
if ((*subdm)->nullspaceConstructors[f]) {
haveNull = PETSC_TRUE;
nf = f;
}
}
if (haveNull) {
MatNullSpace nullSpace;
ierr = (*(*subdm)->nullspaceConstructors[nf])(*subdm, nf, &nullSpace);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) nullSpace);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
}
if (dm->fields) {
if (nF != dm->numFields) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "The number of DM fields %d does not match the number of Section fields %d", dm->numFields, nF);
ierr = DMSetNumFields(*subdm, numFields);CHKERRQ(ierr);
for (f = 0; f < numFields; ++f) {
ierr = PetscObjectListDuplicate(dm->fields[fields[f]]->olist, &(*subdm)->fields[f]->olist);CHKERRQ(ierr);
}
if (numFields == 1) {
MatNullSpace space;
Mat pmat;
ierr = PetscObjectQuery((*subdm)->fields[0], "nullspace", (PetscObject*) &space);CHKERRQ(ierr);
if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) space);CHKERRQ(ierr);}
ierr = PetscObjectQuery((*subdm)->fields[0], "nearnullspace", (PetscObject*) &space);CHKERRQ(ierr);
if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nearnullspace", (PetscObject) space);CHKERRQ(ierr);}
ierr = PetscObjectQuery((*subdm)->fields[0], "pmat", (PetscObject*) &pmat);CHKERRQ(ierr);
if (pmat) {ierr = PetscObjectCompose((PetscObject) *is, "pmat", (PetscObject) pmat);CHKERRQ(ierr);}
}
}
}
PetscFunctionReturn(0);
}
/* This assumes that the DM has been cloned prior to the call */
PetscErrorCode DMCreateSubDM_Section_Private(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm)
{
PetscSection section, sectionGlobal;
PetscInt *subIndices;
PetscInt subSize = 0, subOff = 0, nF, f, pStart, pEnd, p;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!numFields) PetscFunctionReturn(0);
ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);
ierr = DMGetDefaultGlobalSection(dm, §ionGlobal);CHKERRQ(ierr);
if (!section) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default section for DM before splitting fields");
if (!sectionGlobal) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default global section for DM before splitting fields");
ierr = PetscSectionGetNumFields(section, &nF);CHKERRQ(ierr);
if (numFields > nF) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Number of requested fields %d greater than number of DM fields %d", numFields, nF);
if (is) {
ierr = PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt gdof;
ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr);
if (gdof > 0) {
for (f = 0; f < numFields; ++f) {
PetscInt fdof, fcdof;
ierr = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr);
ierr = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr);
subSize += fdof-fcdof;
}
}
}
ierr = PetscMalloc1(subSize, &subIndices);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt gdof, goff;
ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr);
if (gdof > 0) {
ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
for (f = 0; f < numFields; ++f) {
PetscInt fdof, fcdof, fc, f2, poff = 0;
/* Can get rid of this loop by storing field information in the global section */
for (f2 = 0; f2 < fields[f]; ++f2) {
ierr = PetscSectionGetFieldDof(section, p, f2, &fdof);CHKERRQ(ierr);
ierr = PetscSectionGetFieldConstraintDof(section, p, f2, &fcdof);CHKERRQ(ierr);
poff += fdof-fcdof;
}
ierr = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr);
ierr = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr);
for (fc = 0; fc < fdof-fcdof; ++fc, ++subOff) {
subIndices[subOff] = goff+poff+fc;
}
}
}
}
ierr = ISCreateGeneral(PetscObjectComm((PetscObject)dm), subSize, subIndices, PETSC_OWN_POINTER, is);CHKERRQ(ierr);
}
if (subdm) {
PetscSection subsection;
PetscBool haveNull = PETSC_FALSE;
PetscInt f, nf = 0;
ierr = PetscSectionCreateSubsection(section, numFields, fields, &subsection);CHKERRQ(ierr);
ierr = DMSetDefaultSection(*subdm, subsection);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&subsection);CHKERRQ(ierr);
for (f = 0; f < numFields; ++f) {
(*subdm)->nullspaceConstructors[f] = dm->nullspaceConstructors[fields[f]];
if ((*subdm)->nullspaceConstructors[f]) {
haveNull = PETSC_TRUE;
nf = f;
}
}
if (haveNull && is) {
MatNullSpace nullSpace;
ierr = (*(*subdm)->nullspaceConstructors[nf])(*subdm, nf, &nullSpace);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) nullSpace);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
}
if (dm->prob) {
PetscInt Nf;
ierr = PetscDSGetNumFields(dm->prob, &Nf);CHKERRQ(ierr);
if (nF != Nf) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "The number of DM fields %d does not match the number of Section fields %d", Nf, nF);
ierr = DMSetNumFields(*subdm, numFields);CHKERRQ(ierr);
for (f = 0; f < numFields; ++f) {
PetscObject disc;
ierr = DMGetField(dm, fields[f], &disc);CHKERRQ(ierr);
ierr = DMSetField(*subdm, f, disc);CHKERRQ(ierr);
}
if (numFields == 1 && is) {
PetscObject disc, space, pmat;
ierr = DMGetField(*subdm, 0, &disc);CHKERRQ(ierr);
ierr = PetscObjectQuery(disc, "nullspace", &space);CHKERRQ(ierr);
if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nullspace", space);CHKERRQ(ierr);}
ierr = PetscObjectQuery(disc, "nearnullspace", &space);CHKERRQ(ierr);
if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nearnullspace", space);CHKERRQ(ierr);}
ierr = PetscObjectQuery(disc, "pmat", &pmat);CHKERRQ(ierr);
if (pmat) {ierr = PetscObjectCompose((PetscObject) *is, "pmat", pmat);CHKERRQ(ierr);}
}
}
}
#if 0
/* We need a way to filter the original SF for given fields:
- Keeping the original section around it too much I think
- We could keep the distributed section, and subset it
*/
if (dm->sfNatural) {
PetscSF sfNatural;
ierr = PetscSectionCreateSubsection(dm->originalSection, numFields, fields, &(*subdm)->originalSection);CHKERRQ(ierr);
ierr = DMPlexCreateGlobalToNaturalPetscSF(*subdm, &sfNatural);CHKERRQ(ierr);
ierr = DMPlexSetGlobalToNaturalPetscSF(*subdm, sfNatural);CHKERRQ(ierr);
}
#endif
PetscFunctionReturn(0);
}
PetscErrorCode DMPlexPreallocateOperator(DM dm, PetscInt bs, PetscSection section, PetscSection sectionGlobal, PetscInt dnz[], PetscInt onz[], PetscInt dnzu[], PetscInt onzu[], Mat A, PetscBool fillMatrix)
{
MPI_Comm comm;
MatType mtype;
PetscSF sf, sfDof, sfAdj;
PetscSection leafSectionAdj, rootSectionAdj, sectionAdj, anchorSectionAdj;
PetscInt nroots, nleaves, l, p;
const PetscInt *leaves;
const PetscSFNode *remotes;
PetscInt dim, pStart, pEnd, numDof, globalOffStart, globalOffEnd, numCols;
PetscInt *tmpAdj = NULL, *adj, *rootAdj, *anchorAdj = NULL, *cols, *remoteOffsets;
PetscInt adjSize;
PetscLayout rLayout;
PetscInt locRows, rStart, rEnd, r;
PetscMPIInt size;
PetscBool doCommLocal, doComm, debug = PETSC_FALSE, isSymBlock, isSymSeqBlock, isSymMPIBlock;
PetscBool useAnchors;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 3);
PetscValidHeaderSpecific(sectionGlobal, PETSC_SECTION_CLASSID, 4);
PetscValidHeaderSpecific(A, MAT_CLASSID, 9);
if (dnz) PetscValidPointer(dnz,5);
if (onz) PetscValidPointer(onz,6);
if (dnzu) PetscValidPointer(dnzu,7);
if (onzu) PetscValidPointer(onzu,8);
ierr = PetscLogEventBegin(DMPLEX_Preallocate,dm,0,0,0);CHKERRQ(ierr);
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL, "-dm_view_preallocation", &debug, NULL);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr);
ierr = PetscSFGetGraph(sf, &nroots, NULL, NULL, NULL);CHKERRQ(ierr);
doCommLocal = (size > 1) && (nroots >= 0) ? PETSC_TRUE : PETSC_FALSE;
ierr = MPI_Allreduce(&doCommLocal, &doComm, 1, MPIU_BOOL, MPI_LAND, comm);CHKERRQ(ierr);
/* Create dof SF based on point SF */
if (debug) {
ierr = PetscPrintf(comm, "Input Section for Preallocation:\n");CHKERRQ(ierr);
ierr = PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Input Global Section for Preallocation:\n");CHKERRQ(ierr);
ierr = PetscSectionView(sectionGlobal, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Input SF for Preallocation:\n");CHKERRQ(ierr);
ierr = PetscSFView(sf, NULL);CHKERRQ(ierr);
}
ierr = PetscSFCreateRemoteOffsets(sf, section, section, &remoteOffsets);CHKERRQ(ierr);
ierr = PetscSFCreateSectionSF(sf, section, remoteOffsets, section, &sfDof);CHKERRQ(ierr);
if (debug) {
ierr = PetscPrintf(comm, "Dof SF for Preallocation:\n");CHKERRQ(ierr);
ierr = PetscSFView(sfDof, NULL);CHKERRQ(ierr);
}
/* Create section for dof adjacency (dof ==> # adj dof) */
ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(section, &numDof);CHKERRQ(ierr);
ierr = PetscSectionCreate(comm, &leafSectionAdj);CHKERRQ(ierr);
ierr = PetscSectionSetChart(leafSectionAdj, 0, numDof);CHKERRQ(ierr);
ierr = PetscSectionCreate(comm, &rootSectionAdj);CHKERRQ(ierr);
ierr = PetscSectionSetChart(rootSectionAdj, 0, numDof);CHKERRQ(ierr);
/* Fill in the ghost dofs on the interface */
ierr = PetscSFGetGraph(sf, NULL, &nleaves, &leaves, &remotes);CHKERRQ(ierr);
/* use constraints in finding adjacency in this routine */
ierr = DMPlexGetAdjacencyUseAnchors(dm,&useAnchors);CHKERRQ(ierr);
ierr = DMPlexSetAdjacencyUseAnchors(dm,PETSC_TRUE);CHKERRQ(ierr);
/*
section - maps points to (# dofs, local dofs)
sectionGlobal - maps points to (# dofs, global dofs)
leafSectionAdj - maps unowned local dofs to # adj dofs
rootSectionAdj - maps owned local dofs to # adj dofs
adj - adj global dofs indexed by leafSectionAdj
rootAdj - adj global dofs indexed by rootSectionAdj
sf - describes shared points across procs
sfDof - describes shared dofs across procs
sfAdj - describes shared adjacent dofs across procs
** The bootstrapping process involves six rounds with similar structure of visiting neighbors of each point.
(0). If there are point-to-point constraints, add the adjacencies of constrained points to anchors in anchorAdj
(This is done in DMPlexComputeAnchorAdjacencies())
1. Visit unowned points on interface, count adjacencies placing in leafSectionAdj
Reduce those counts to rootSectionAdj (now redundantly counting some interface points)
2. Visit owned points on interface, count adjacencies placing in rootSectionAdj
Create sfAdj connecting rootSectionAdj and leafSectionAdj
3. Visit unowned points on interface, write adjacencies to adj
Gather adj to rootAdj (note that there is redundancy in rootAdj when multiple procs find the same adjacencies)
4. Visit owned points on interface, write adjacencies to rootAdj
Remove redundancy in rootAdj
** The last two traversals use transitive closure
5. Visit all owned points in the subdomain, count dofs for each point (sectionAdj)
Allocate memory addressed by sectionAdj (cols)
6. Visit all owned points in the subdomain, insert dof adjacencies into cols
** Knowing all the column adjacencies, check ownership and sum into dnz and onz
*/
ierr = DMPlexComputeAnchorAdjacencies(dm,section,sectionGlobal,&anchorSectionAdj,&anchorAdj);CHKERRQ(ierr);
for (l = 0; l < nleaves; ++l) {
PetscInt dof, off, d, q, anDof;
PetscInt p = leaves[l], numAdj = PETSC_DETERMINE;
if ((p < pStart) || (p >= pEnd)) continue;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
for (q = 0; q < numAdj; ++q) {
const PetscInt padj = tmpAdj[q];
PetscInt ndof, ncdof;
if ((padj < pStart) || (padj >= pEnd)) continue;
ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
for (d = off; d < off+dof; ++d) {
ierr = PetscSectionAddDof(leafSectionAdj, d, ndof-ncdof);CHKERRQ(ierr);
}
}
ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
if (anDof) {
for (d = off; d < off+dof; ++d) {
ierr = PetscSectionAddDof(leafSectionAdj, d, anDof);CHKERRQ(ierr);
}
}
}
ierr = PetscSectionSetUp(leafSectionAdj);CHKERRQ(ierr);
if (debug) {
ierr = PetscPrintf(comm, "Adjacency Section for Preallocation on Leaves:\n");CHKERRQ(ierr);
ierr = PetscSectionView(leafSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Get maximum remote adjacency sizes for owned dofs on interface (roots) */
if (doComm) {
ierr = PetscSFReduceBegin(sfDof, MPIU_INT, leafSectionAdj->atlasDof, rootSectionAdj->atlasDof, MPI_SUM);CHKERRQ(ierr);
ierr = PetscSFReduceEnd(sfDof, MPIU_INT, leafSectionAdj->atlasDof, rootSectionAdj->atlasDof, MPI_SUM);CHKERRQ(ierr);
}
if (debug) {
ierr = PetscPrintf(comm, "Adjancency Section for Preallocation on Roots:\n");CHKERRQ(ierr);
ierr = PetscSectionView(rootSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Add in local adjacency sizes for owned dofs on interface (roots) */
for (p = pStart; p < pEnd; ++p) {
PetscInt numAdj = PETSC_DETERMINE, adof, dof, off, d, q, anDof;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
if (!dof) continue;
ierr = PetscSectionGetDof(rootSectionAdj, off, &adof);CHKERRQ(ierr);
if (adof <= 0) continue;
ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
for (q = 0; q < numAdj; ++q) {
const PetscInt padj = tmpAdj[q];
PetscInt ndof, ncdof;
if ((padj < pStart) || (padj >= pEnd)) continue;
ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
for (d = off; d < off+dof; ++d) {
ierr = PetscSectionAddDof(rootSectionAdj, d, ndof-ncdof);CHKERRQ(ierr);
}
}
ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
if (anDof) {
for (d = off; d < off+dof; ++d) {
ierr = PetscSectionAddDof(rootSectionAdj, d, anDof);CHKERRQ(ierr);
}
}
}
ierr = PetscSectionSetUp(rootSectionAdj);CHKERRQ(ierr);
if (debug) {
ierr = PetscPrintf(comm, "Adjancency Section for Preallocation on Roots after local additions:\n");CHKERRQ(ierr);
ierr = PetscSectionView(rootSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Create adj SF based on dof SF */
ierr = PetscSFCreateRemoteOffsets(sfDof, rootSectionAdj, leafSectionAdj, &remoteOffsets);CHKERRQ(ierr);
ierr = PetscSFCreateSectionSF(sfDof, rootSectionAdj, remoteOffsets, leafSectionAdj, &sfAdj);CHKERRQ(ierr);
if (debug) {
ierr = PetscPrintf(comm, "Adjacency SF for Preallocation:\n");CHKERRQ(ierr);
ierr = PetscSFView(sfAdj, NULL);CHKERRQ(ierr);
}
ierr = PetscSFDestroy(&sfDof);CHKERRQ(ierr);
/* Create leaf adjacency */
ierr = PetscSectionSetUp(leafSectionAdj);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(leafSectionAdj, &adjSize);CHKERRQ(ierr);
ierr = PetscCalloc1(adjSize, &adj);CHKERRQ(ierr);
for (l = 0; l < nleaves; ++l) {
PetscInt dof, off, d, q, anDof, anOff;
PetscInt p = leaves[l], numAdj = PETSC_DETERMINE;
if ((p < pStart) || (p >= pEnd)) continue;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(anchorSectionAdj, p, &anOff);CHKERRQ(ierr);
for (d = off; d < off+dof; ++d) {
PetscInt aoff, i = 0;
ierr = PetscSectionGetOffset(leafSectionAdj, d, &aoff);CHKERRQ(ierr);
for (q = 0; q < numAdj; ++q) {
const PetscInt padj = tmpAdj[q];
PetscInt ndof, ncdof, ngoff, nd;
if ((padj < pStart) || (padj >= pEnd)) continue;
ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionGlobal, padj, &ngoff);CHKERRQ(ierr);
for (nd = 0; nd < ndof-ncdof; ++nd) {
adj[aoff+i] = (ngoff < 0 ? -(ngoff+1) : ngoff) + nd;
++i;
}
}
for (q = 0; q < anDof; q++) {
adj[aoff+i] = anchorAdj[anOff+q];
++i;
}
}
}
/* Debugging */
if (debug) {
IS tmp;
ierr = PetscPrintf(comm, "Leaf adjacency indices\n");CHKERRQ(ierr);
ierr = ISCreateGeneral(comm, adjSize, adj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
ierr = ISView(tmp, NULL);CHKERRQ(ierr);
ierr = ISDestroy(&tmp);CHKERRQ(ierr);
}
/* Gather adjacent indices to root */
ierr = PetscSectionGetStorageSize(rootSectionAdj, &adjSize);CHKERRQ(ierr);
ierr = PetscMalloc1(adjSize, &rootAdj);CHKERRQ(ierr);
for (r = 0; r < adjSize; ++r) rootAdj[r] = -1;
if (doComm) {
const PetscInt *indegree;
PetscInt *remoteadj, radjsize = 0;
ierr = PetscSFComputeDegreeBegin(sfAdj, &indegree);CHKERRQ(ierr);
ierr = PetscSFComputeDegreeEnd(sfAdj, &indegree);CHKERRQ(ierr);
for (p = 0; p < adjSize; ++p) radjsize += indegree[p];
ierr = PetscMalloc1(radjsize, &remoteadj);CHKERRQ(ierr);
ierr = PetscSFGatherBegin(sfAdj, MPIU_INT, adj, remoteadj);CHKERRQ(ierr);
ierr = PetscSFGatherEnd(sfAdj, MPIU_INT, adj, remoteadj);CHKERRQ(ierr);
for (p = 0, l = 0, r = 0; p < adjSize; ++p, l = PetscMax(p, l + indegree[p-1])) {
PetscInt s;
for (s = 0; s < indegree[p]; ++s, ++r) rootAdj[l+s] = remoteadj[r];
}
if (r != radjsize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Inconsistency in communication %d != %d", r, radjsize);
if (l != adjSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Inconsistency in communication %d != %d", l, adjSize);
ierr = PetscFree(remoteadj);CHKERRQ(ierr);
}
ierr = PetscSFDestroy(&sfAdj);CHKERRQ(ierr);
ierr = PetscFree(adj);CHKERRQ(ierr);
/* Debugging */
if (debug) {
IS tmp;
ierr = PetscPrintf(comm, "Root adjacency indices after gather\n");CHKERRQ(ierr);
ierr = ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
ierr = ISView(tmp, NULL);CHKERRQ(ierr);
ierr = ISDestroy(&tmp);CHKERRQ(ierr);
}
/* Add in local adjacency indices for owned dofs on interface (roots) */
for (p = pStart; p < pEnd; ++p) {
PetscInt numAdj = PETSC_DETERMINE, adof, dof, off, d, q, anDof, anOff;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
if (!dof) continue;
ierr = PetscSectionGetDof(rootSectionAdj, off, &adof);CHKERRQ(ierr);
if (adof <= 0) continue;
ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(anchorSectionAdj, p, &anOff);CHKERRQ(ierr);
for (d = off; d < off+dof; ++d) {
PetscInt adof, aoff, i;
ierr = PetscSectionGetDof(rootSectionAdj, d, &adof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(rootSectionAdj, d, &aoff);CHKERRQ(ierr);
i = adof-1;
for (q = 0; q < anDof; q++) {
rootAdj[aoff+i] = anchorAdj[anOff+q];
--i;
}
for (q = 0; q < numAdj; ++q) {
const PetscInt padj = tmpAdj[q];
PetscInt ndof, ncdof, ngoff, nd;
if ((padj < pStart) || (padj >= pEnd)) continue;
ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionGlobal, padj, &ngoff);CHKERRQ(ierr);
for (nd = 0; nd < ndof-ncdof; ++nd) {
rootAdj[aoff+i] = ngoff < 0 ? -(ngoff+1)+nd : ngoff+nd;
--i;
}
}
}
}
/* Debugging */
if (debug) {
IS tmp;
ierr = PetscPrintf(comm, "Root adjacency indices\n");CHKERRQ(ierr);
ierr = ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
ierr = ISView(tmp, NULL);CHKERRQ(ierr);
ierr = ISDestroy(&tmp);CHKERRQ(ierr);
}
/* Compress indices */
ierr = PetscSectionSetUp(rootSectionAdj);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt dof, cdof, off, d;
PetscInt adof, aoff;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
if (!dof) continue;
ierr = PetscSectionGetDof(rootSectionAdj, off, &adof);CHKERRQ(ierr);
if (adof <= 0) continue;
for (d = off; d < off+dof-cdof; ++d) {
ierr = PetscSectionGetDof(rootSectionAdj, d, &adof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(rootSectionAdj, d, &aoff);CHKERRQ(ierr);
ierr = PetscSortRemoveDupsInt(&adof, &rootAdj[aoff]);CHKERRQ(ierr);
ierr = PetscSectionSetDof(rootSectionAdj, d, adof);CHKERRQ(ierr);
}
}
/* Debugging */
if (debug) {
IS tmp;
ierr = PetscPrintf(comm, "Adjancency Section for Preallocation on Roots after compression:\n");CHKERRQ(ierr);
ierr = PetscSectionView(rootSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Root adjacency indices after compression\n");CHKERRQ(ierr);
ierr = ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
ierr = ISView(tmp, NULL);CHKERRQ(ierr);
ierr = ISDestroy(&tmp);CHKERRQ(ierr);
}
/* Build adjacency section: Maps global indices to sets of adjacent global indices */
ierr = PetscSectionGetOffsetRange(sectionGlobal, &globalOffStart, &globalOffEnd);CHKERRQ(ierr);
ierr = PetscSectionCreate(comm, §ionAdj);CHKERRQ(ierr);
ierr = PetscSectionSetChart(sectionAdj, globalOffStart, globalOffEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt numAdj = PETSC_DETERMINE, dof, cdof, off, goff, d, q, anDof;
PetscBool found = PETSC_TRUE;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
for (d = 0; d < dof-cdof; ++d) {
PetscInt ldof, rdof;
ierr = PetscSectionGetDof(leafSectionAdj, off+d, &ldof);CHKERRQ(ierr);
ierr = PetscSectionGetDof(rootSectionAdj, off+d, &rdof);CHKERRQ(ierr);
if (ldof > 0) {
/* We do not own this point */
} else if (rdof > 0) {
ierr = PetscSectionSetDof(sectionAdj, goff+d, rdof);CHKERRQ(ierr);
} else {
found = PETSC_FALSE;
}
}
if (found) continue;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
for (q = 0; q < numAdj; ++q) {
const PetscInt padj = tmpAdj[q];
PetscInt ndof, ncdof, noff;
if ((padj < pStart) || (padj >= pEnd)) continue;
ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, padj, &noff);CHKERRQ(ierr);
for (d = goff; d < goff+dof-cdof; ++d) {
ierr = PetscSectionAddDof(sectionAdj, d, ndof-ncdof);CHKERRQ(ierr);
}
}
ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
if (anDof) {
for (d = goff; d < goff+dof-cdof; ++d) {
ierr = PetscSectionAddDof(sectionAdj, d, anDof);CHKERRQ(ierr);
}
}
}
ierr = PetscSectionSetUp(sectionAdj);CHKERRQ(ierr);
if (debug) {
ierr = PetscPrintf(comm, "Adjacency Section for Preallocation:\n");CHKERRQ(ierr);
ierr = PetscSectionView(sectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Get adjacent indices */
ierr = PetscSectionGetStorageSize(sectionAdj, &numCols);CHKERRQ(ierr);
ierr = PetscMalloc1(numCols, &cols);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt numAdj = PETSC_DETERMINE, dof, cdof, off, goff, d, q, anDof, anOff;
PetscBool found = PETSC_TRUE;
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
for (d = 0; d < dof-cdof; ++d) {
PetscInt ldof, rdof;
ierr = PetscSectionGetDof(leafSectionAdj, off+d, &ldof);CHKERRQ(ierr);
ierr = PetscSectionGetDof(rootSectionAdj, off+d, &rdof);CHKERRQ(ierr);
if (ldof > 0) {
/* We do not own this point */
} else if (rdof > 0) {
PetscInt aoff, roff;
ierr = PetscSectionGetOffset(sectionAdj, goff+d, &aoff);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(rootSectionAdj, off+d, &roff);CHKERRQ(ierr);
ierr = PetscMemcpy(&cols[aoff], &rootAdj[roff], rdof * sizeof(PetscInt));CHKERRQ(ierr);
} else {
found = PETSC_FALSE;
}
}
if (found) continue;
ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(anchorSectionAdj, p, &anOff);CHKERRQ(ierr);
for (d = goff; d < goff+dof-cdof; ++d) {
PetscInt adof, aoff, i = 0;
ierr = PetscSectionGetDof(sectionAdj, d, &adof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionAdj, d, &aoff);CHKERRQ(ierr);
for (q = 0; q < numAdj; ++q) {
const PetscInt padj = tmpAdj[q];
PetscInt ndof, ncdof, ngoff, nd;
const PetscInt *ncind;
/* Adjacent points may not be in the section chart */
if ((padj < pStart) || (padj >= pEnd)) continue;
ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintIndices(section, padj, &ncind);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionGlobal, padj, &ngoff);CHKERRQ(ierr);
for (nd = 0; nd < ndof-ncdof; ++nd, ++i) {
cols[aoff+i] = ngoff < 0 ? -(ngoff+1)+nd : ngoff+nd;
}
}
for (q = 0; q < anDof; q++, i++) {
cols[aoff+i] = anchorAdj[anOff + q];
}
if (i != adof) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of entries %D != %D for dof %D (point %D)", i, adof, d, p);
}
}
ierr = PetscSectionDestroy(&anchorSectionAdj);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&leafSectionAdj);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&rootSectionAdj);CHKERRQ(ierr);
ierr = PetscFree(anchorAdj);CHKERRQ(ierr);
ierr = PetscFree(rootAdj);CHKERRQ(ierr);
ierr = PetscFree(tmpAdj);CHKERRQ(ierr);
/* Debugging */
if (debug) {
IS tmp;
ierr = PetscPrintf(comm, "Column indices\n");CHKERRQ(ierr);
ierr = ISCreateGeneral(comm, numCols, cols, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
ierr = ISView(tmp, NULL);CHKERRQ(ierr);
ierr = ISDestroy(&tmp);CHKERRQ(ierr);
}
/* Create allocation vectors from adjacency graph */
ierr = MatGetLocalSize(A, &locRows, NULL);CHKERRQ(ierr);
ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)A), &rLayout);CHKERRQ(ierr);
ierr = PetscLayoutSetLocalSize(rLayout, locRows);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(rLayout, 1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(rLayout);CHKERRQ(ierr);
ierr = PetscLayoutGetRange(rLayout, &rStart, &rEnd);CHKERRQ(ierr);
ierr = PetscLayoutDestroy(&rLayout);CHKERRQ(ierr);
/* Only loop over blocks of rows */
if (rStart%bs || rEnd%bs) SETERRQ3(PetscObjectComm((PetscObject)A), PETSC_ERR_ARG_WRONG, "Invalid layout [%d, %d) for matrix, must be divisible by block size %d", rStart, rEnd, bs);
for (r = rStart/bs; r < rEnd/bs; ++r) {
const PetscInt row = r*bs;
PetscInt numCols, cStart, c;
ierr = PetscSectionGetDof(sectionAdj, row, &numCols);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionAdj, row, &cStart);CHKERRQ(ierr);
for (c = cStart; c < cStart+numCols; ++c) {
if ((cols[c] >= rStart*bs) && (cols[c] < rEnd*bs)) {
++dnz[r-rStart];
if (cols[c] >= row) ++dnzu[r-rStart];
} else {
++onz[r-rStart];
if (cols[c] >= row) ++onzu[r-rStart];
}
}
}
if (bs > 1) {
for (r = 0; r < locRows/bs; ++r) {
dnz[r] /= bs;
onz[r] /= bs;
dnzu[r] /= bs;
onzu[r] /= bs;
}
}
/* Set matrix pattern */
ierr = MatXAIJSetPreallocation(A, bs, dnz, onz, dnzu, onzu);CHKERRQ(ierr);
ierr = MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
/* Check for symmetric storage */
ierr = MatGetType(A, &mtype);CHKERRQ(ierr);
ierr = PetscStrcmp(mtype, MATSBAIJ, &isSymBlock);CHKERRQ(ierr);
ierr = PetscStrcmp(mtype, MATSEQSBAIJ, &isSymSeqBlock);CHKERRQ(ierr);
ierr = PetscStrcmp(mtype, MATMPISBAIJ, &isSymMPIBlock);CHKERRQ(ierr);
if (isSymBlock || isSymSeqBlock || isSymMPIBlock) {ierr = MatSetOption(A, MAT_IGNORE_LOWER_TRIANGULAR, PETSC_TRUE);CHKERRQ(ierr);}
/* Fill matrix with zeros */
if (fillMatrix) {
PetscScalar *values;
PetscInt maxRowLen = 0;
for (r = rStart; r < rEnd; ++r) {
PetscInt len;
ierr = PetscSectionGetDof(sectionAdj, r, &len);CHKERRQ(ierr);
maxRowLen = PetscMax(maxRowLen, len);
}
ierr = PetscCalloc1(maxRowLen, &values);CHKERRQ(ierr);
for (r = rStart; r < rEnd; ++r) {
PetscInt numCols, cStart;
ierr = PetscSectionGetDof(sectionAdj, r, &numCols);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionAdj, r, &cStart);CHKERRQ(ierr);
ierr = MatSetValues(A, 1, &r, numCols, &cols[cStart], values, INSERT_VALUES);CHKERRQ(ierr);
}
ierr = PetscFree(values);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
/* restore original useAnchors */
ierr = DMPlexSetAdjacencyUseAnchors(dm,useAnchors);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ionAdj);CHKERRQ(ierr);
ierr = PetscFree(cols);CHKERRQ(ierr);
ierr = PetscLogEventEnd(DMPLEX_Preallocate,dm,0,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMLabelDistribute(DMLabel label, PetscSF sf, DMLabel *labelNew)
{
MPI_Comm comm;
PetscSection rootSection, leafSection;
PetscSF labelSF;
PetscInt p, pStart, pEnd, l, lStart, lEnd, s, nroots, nleaves, size, dof, offset, stratum;
PetscInt *remoteOffsets, *rootStrata, *rootIdx, *leafStrata, *strataIdx;
char *name;
PetscInt nameSize;
size_t len = 0;
PetscMPIInt rank, numProcs;
PetscErrorCode ierr;
PetscFunctionBegin;
if (label) {ierr = DMLabelMakeAllValid_Private(label);CHKERRQ(ierr);}
ierr = PetscObjectGetComm((PetscObject)sf, &comm);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
/* Bcast name */
if (!rank) {ierr = PetscStrlen(label->name, &len);CHKERRQ(ierr);}
nameSize = len;
ierr = MPI_Bcast(&nameSize, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
ierr = PetscMalloc1(nameSize+1, &name);CHKERRQ(ierr);
if (!rank) {ierr = PetscMemcpy(name, label->name, nameSize+1);CHKERRQ(ierr);}
ierr = MPI_Bcast(name, nameSize+1, MPI_CHAR, 0, comm);CHKERRQ(ierr);
ierr = DMLabelCreate(name, labelNew);CHKERRQ(ierr);
ierr = PetscFree(name);CHKERRQ(ierr);
/* Bcast numStrata */
if (!rank) (*labelNew)->numStrata = label->numStrata;
ierr = MPI_Bcast(&(*labelNew)->numStrata, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
/* Bcast stratumValues */
ierr = PetscMalloc1((*labelNew)->numStrata, &(*labelNew)->stratumValues);CHKERRQ(ierr);
if (!rank) {ierr = PetscMemcpy((*labelNew)->stratumValues, label->stratumValues, label->numStrata * sizeof(PetscInt));CHKERRQ(ierr);}
ierr = MPI_Bcast((*labelNew)->stratumValues, (*labelNew)->numStrata, MPIU_INT, 0, comm);CHKERRQ(ierr);
ierr = PetscMalloc1((*labelNew)->numStrata, &(*labelNew)->arrayValid);CHKERRQ(ierr);
for (s = 0; s < (*labelNew)->numStrata; ++s) (*labelNew)->arrayValid[s] = PETSC_TRUE;
/* Build a section detailing strata-per-point, distribute and build SF
from that and then send our points. */
ierr = PetscSFGetGraph(sf, &nroots, &nleaves, NULL, NULL);CHKERRQ(ierr);
ierr = PetscSectionCreate(comm, &rootSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(rootSection, 0, nroots);CHKERRQ(ierr);
if (label) {
for (s = 0; s < label->numStrata; ++s) {
lStart = 0;
lEnd = label->stratumSizes[s];
for (l=lStart; l<lEnd; l++) {
ierr = PetscSectionGetDof(rootSection, label->points[s][l], &dof);CHKERRQ(ierr);
ierr = PetscSectionSetDof(rootSection, label->points[s][l], dof+1);CHKERRQ(ierr);
}
}
}
ierr = PetscSectionSetUp(rootSection);CHKERRQ(ierr);
/* Create a point-wise array of point strata */
ierr = PetscSectionGetStorageSize(rootSection, &size);CHKERRQ(ierr);
ierr = PetscMalloc1(size, &rootStrata);CHKERRQ(ierr);
ierr = PetscCalloc1(nroots, &rootIdx);CHKERRQ(ierr);
if (label) {
for (s = 0; s < label->numStrata; ++s) {
lStart = 0;
lEnd = label->stratumSizes[s];
for (l=lStart; l<lEnd; l++) {
p = label->points[s][l];
ierr = PetscSectionGetOffset(rootSection, p, &offset);CHKERRQ(ierr);
rootStrata[offset+rootIdx[p]++] = s;
}
}
}
/* Build SF that maps label points to remote processes */
ierr = PetscSectionCreate(comm, &leafSection);CHKERRQ(ierr);
ierr = PetscSFDistributeSection(sf, rootSection, &remoteOffsets, leafSection);CHKERRQ(ierr);
ierr = PetscSFCreateSectionSF(sf, rootSection, remoteOffsets, leafSection, &labelSF);CHKERRQ(ierr);
/* Send the strata for each point over the derived SF */
ierr = PetscSectionGetStorageSize(leafSection, &size);CHKERRQ(ierr);
ierr = PetscMalloc1(size, &leafStrata);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(labelSF, MPIU_INT, rootStrata, leafStrata);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(labelSF, MPIU_INT, rootStrata, leafStrata);CHKERRQ(ierr);
/* Rebuild the point strata on the receiver */
ierr = PetscCalloc1((*labelNew)->numStrata,&(*labelNew)->stratumSizes);CHKERRQ(ierr);
ierr = PetscSectionGetChart(leafSection, &pStart, &pEnd);CHKERRQ(ierr);
for (p=pStart; p<pEnd; p++) {
ierr = PetscSectionGetDof(leafSection, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(leafSection, p, &offset);CHKERRQ(ierr);
for (s=0; s<dof; s++) {
(*labelNew)->stratumSizes[leafStrata[offset+s]]++;
}
}
ierr = PetscCalloc1((*labelNew)->numStrata,&(*labelNew)->ht);CHKERRQ(ierr);
ierr = PetscMalloc1((*labelNew)->numStrata,&(*labelNew)->points);CHKERRQ(ierr);
for (s = 0; s < (*labelNew)->numStrata; ++s) {
PetscHashICreate((*labelNew)->ht[s]);
ierr = PetscMalloc1((*labelNew)->stratumSizes[s], &(*labelNew)->points[s]);CHKERRQ(ierr);
}
/* Insert points into new strata */
ierr = PetscCalloc1((*labelNew)->numStrata, &strataIdx);CHKERRQ(ierr);
ierr = PetscSectionGetChart(leafSection, &pStart, &pEnd);CHKERRQ(ierr);
for (p=pStart; p<pEnd; p++) {
ierr = PetscSectionGetDof(leafSection, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(leafSection, p, &offset);CHKERRQ(ierr);
for (s=0; s<dof; s++) {
stratum = leafStrata[offset+s];
(*labelNew)->points[stratum][strataIdx[stratum]++] = p;
}
}
ierr = PetscFree(rootStrata);CHKERRQ(ierr);
ierr = PetscFree(leafStrata);CHKERRQ(ierr);
ierr = PetscFree(rootIdx);CHKERRQ(ierr);
ierr = PetscFree(strataIdx);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&rootSection);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&leafSection);CHKERRQ(ierr);
ierr = PetscSFDestroy(&labelSF);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMLabelDistribute_Internal(DMLabel label, PetscSF sf, PetscSection *leafSection, PetscInt **leafStrata)
{
MPI_Comm comm;
PetscInt s, l, nroots, nleaves, dof, offset, size;
PetscInt *remoteOffsets, *rootStrata, *rootIdx;
PetscSection rootSection;
PetscSF labelSF;
PetscErrorCode ierr;
PetscFunctionBegin;
if (label) {ierr = DMLabelMakeAllValid_Private(label);CHKERRQ(ierr);}
ierr = PetscObjectGetComm((PetscObject)sf, &comm);CHKERRQ(ierr);
/* Build a section of stratum values per point, generate the according SF
and distribute point-wise stratum values to leaves. */
ierr = PetscSFGetGraph(sf, &nroots, &nleaves, NULL, NULL);CHKERRQ(ierr);
ierr = PetscSectionCreate(comm, &rootSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(rootSection, 0, nroots);CHKERRQ(ierr);
if (label) {
for (s = 0; s < label->numStrata; ++s) {
const PetscInt *points;
ierr = ISGetIndices(label->points[s], &points);CHKERRQ(ierr);
for (l = 0; l < label->stratumSizes[s]; l++) {
ierr = PetscSectionGetDof(rootSection, points[l], &dof);CHKERRQ(ierr);
ierr = PetscSectionSetDof(rootSection, points[l], dof+1);CHKERRQ(ierr);
}
ierr = ISRestoreIndices(label->points[s], &points);CHKERRQ(ierr);
}
}
ierr = PetscSectionSetUp(rootSection);CHKERRQ(ierr);
/* Create a point-wise array of stratum values */
ierr = PetscSectionGetStorageSize(rootSection, &size);CHKERRQ(ierr);
ierr = PetscMalloc1(size, &rootStrata);CHKERRQ(ierr);
ierr = PetscCalloc1(nroots, &rootIdx);CHKERRQ(ierr);
if (label) {
for (s = 0; s < label->numStrata; ++s) {
const PetscInt *points;
ierr = ISGetIndices(label->points[s], &points);CHKERRQ(ierr);
for (l = 0; l < label->stratumSizes[s]; l++) {
const PetscInt p = points[l];
ierr = PetscSectionGetOffset(rootSection, p, &offset);CHKERRQ(ierr);
rootStrata[offset+rootIdx[p]++] = label->stratumValues[s];
}
ierr = ISRestoreIndices(label->points[s], &points);CHKERRQ(ierr);
}
}
/* Build SF that maps label points to remote processes */
ierr = PetscSectionCreate(comm, leafSection);CHKERRQ(ierr);
ierr = PetscSFDistributeSection(sf, rootSection, &remoteOffsets, *leafSection);CHKERRQ(ierr);
ierr = PetscSFCreateSectionSF(sf, rootSection, remoteOffsets, *leafSection, &labelSF);CHKERRQ(ierr);
ierr = PetscFree(remoteOffsets);CHKERRQ(ierr);
/* Send the strata for each point over the derived SF */
ierr = PetscSectionGetStorageSize(*leafSection, &size);CHKERRQ(ierr);
ierr = PetscMalloc1(size, leafStrata);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(labelSF, MPIU_INT, rootStrata, *leafStrata);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(labelSF, MPIU_INT, rootStrata, *leafStrata);CHKERRQ(ierr);
/* Clean up */
ierr = PetscFree(rootStrata);CHKERRQ(ierr);
ierr = PetscFree(rootIdx);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&rootSection);CHKERRQ(ierr);
ierr = PetscSFDestroy(&labelSF);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode TestVecClosure(DM dm, PetscBool useIndex, PetscBool useSpectral, AppCtx *user)
{
PetscSection s;
Vec v;
PetscInt numRuns, cStart, cEnd, c, i;
PetscScalar tmpArray[64];
PetscScalar *userArray = user->reuseArray ? tmpArray : NULL;
PetscReal maxTimePerRun = user->maxVecClosureTime;
PetscLogStage stage;
PetscLogEvent event;
PetscEventPerfInfo eventInfo;
PetscErrorCode ierr;
PetscFunctionBegin;
if (useIndex) {
if (useSpectral) {
ierr = PetscLogStageRegister("DMPlex Vector Closure with Index Test", &stage);CHKERRQ(ierr);
ierr = PetscLogEventRegister("VecClosureInd", PETSC_OBJECT_CLASSID, &event);CHKERRQ(ierr);
} else {
ierr = PetscLogStageRegister("DMPlex Vector Spectral Closure with Index Test", &stage);CHKERRQ(ierr);
ierr = PetscLogEventRegister("VecClosureSpecInd", PETSC_OBJECT_CLASSID, &event);CHKERRQ(ierr);
}
} else {
if (useSpectral) {
ierr = PetscLogStageRegister("DMPlex Vector Spectral Closure Test", &stage);CHKERRQ(ierr);
ierr = PetscLogEventRegister("VecClosureSpec", PETSC_OBJECT_CLASSID, &event);CHKERRQ(ierr);
} else {
ierr = PetscLogStageRegister("DMPlex Vector Closure Test", &stage);CHKERRQ(ierr);
ierr = PetscLogEventRegister("VecClosure", PETSC_OBJECT_CLASSID, &event);CHKERRQ(ierr);
}
}
ierr = PetscLogStagePush(stage);CHKERRQ(ierr);
ierr = DMPlexCreateSection(dm, user->dim, user->numFields, user->numComponents, user->numDof, 0, NULL, NULL, NULL, NULL, &s);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dm, s);CHKERRQ(ierr);
if (useIndex) {ierr = DMPlexCreateClosureIndex(dm, s);CHKERRQ(ierr);}
if (useSpectral) {ierr = DMPlexCreateSpectralClosurePermutation(dm, s);CHKERRQ(ierr);}
ierr = PetscSectionDestroy(&s);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &v);CHKERRQ(ierr);
ierr = PetscLogEventBegin(event,0,0,0,0);CHKERRQ(ierr);
for (i = 0; i < user->iterations; ++i) {
for (c = cStart; c < cEnd; ++c) {
PetscScalar *closure = userArray;
PetscInt closureSize = 64;
ierr = DMPlexVecGetClosure(dm, s, v, c, &closureSize, &closure);CHKERRQ(ierr);
if (!user->reuseArray) {ierr = DMPlexVecRestoreClosure(dm, s, v, c, &closureSize, &closure);CHKERRQ(ierr);}
}
}
ierr = PetscLogEventEnd(event,0,0,0,0);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &v);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = PetscLogEventGetPerfInfo(stage, event, &eventInfo);CHKERRQ(ierr);
numRuns = (cEnd-cStart) * user->iterations;
if (eventInfo.count != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of event calls %d should be %d", eventInfo.count, 1);
if ((PetscInt) eventInfo.flops != 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of event flops %d should be %d", (PetscInt) eventInfo.flops, 0);
if (eventInfo.time > maxTimePerRun * numRuns) {
const char *title = "VecClosures";
const char *titleIndex = "VecClosures with Index";
const char *titleSpec = "VecClosures Spectral";
const char *titleSpecIndex = "VecClosures Spectral with Index";
ierr = PetscPrintf(PETSC_COMM_SELF, "%s: %d Average time per vector closure: %gs standard: %gs\n", useIndex ? (useSpectral ? titleSpecIndex : titleIndex) : (useSpectral ? titleSpec : title), numRuns, eventInfo.time/numRuns, maxTimePerRun);
if (user->errors) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Average time for vector closure %g > standard %g", eventInfo.time/numRuns, maxTimePerRun);
}
PetscFunctionReturn(0);
}
PetscErrorCode DMLabelDistribute(DMLabel label, PetscSF sf, DMLabel *labelNew)
{
MPI_Comm comm;
PetscSection leafSection;
PetscInt p, pStart, pEnd, s, size, dof, offset, stratum;
PetscInt *leafStrata, *strataIdx;
PetscInt **points;
char *name;
PetscInt nameSize;
PetscHashI stratumHash;
PETSC_UNUSED PetscHashIIter ret, iter;
size_t len = 0;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
if (label) {ierr = DMLabelMakeAllValid_Private(label);CHKERRQ(ierr);}
ierr = PetscObjectGetComm((PetscObject)sf, &comm);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
/* Bcast name */
if (!rank) {ierr = PetscStrlen(label->name, &len);CHKERRQ(ierr);}
nameSize = len;
ierr = MPI_Bcast(&nameSize, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
ierr = PetscMalloc1(nameSize+1, &name);CHKERRQ(ierr);
if (!rank) {ierr = PetscMemcpy(name, label->name, nameSize+1);CHKERRQ(ierr);}
ierr = MPI_Bcast(name, nameSize+1, MPI_CHAR, 0, comm);CHKERRQ(ierr);
ierr = DMLabelCreate(name, labelNew);CHKERRQ(ierr);
ierr = PetscFree(name);CHKERRQ(ierr);
/* Bcast defaultValue */
if (!rank) (*labelNew)->defaultValue = label->defaultValue;
ierr = MPI_Bcast(&(*labelNew)->defaultValue, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
/* Distribute stratum values over the SF and get the point mapping on the receiver */
ierr = DMLabelDistribute_Internal(label, sf, &leafSection, &leafStrata);CHKERRQ(ierr);
/* Determine received stratum values and initialise new label*/
PetscHashICreate(stratumHash);
ierr = PetscSectionGetStorageSize(leafSection, &size);CHKERRQ(ierr);
for (p = 0; p < size; ++p) PetscHashIPut(stratumHash, leafStrata[p], ret, iter);
PetscHashISize(stratumHash, (*labelNew)->numStrata);
ierr = PetscMalloc1((*labelNew)->numStrata, &(*labelNew)->validIS);CHKERRQ(ierr);
for (s = 0; s < (*labelNew)->numStrata; ++s) (*labelNew)->validIS[s] = PETSC_TRUE;
ierr = PetscMalloc1((*labelNew)->numStrata, &(*labelNew)->stratumValues);CHKERRQ(ierr);
/* Turn leafStrata into indices rather than stratum values */
offset = 0;
ierr = PetscHashIGetKeys(stratumHash, &offset, (*labelNew)->stratumValues);CHKERRQ(ierr);
for (p = 0; p < size; ++p) {
for (s = 0; s < (*labelNew)->numStrata; ++s) {
if (leafStrata[p] == (*labelNew)->stratumValues[s]) {leafStrata[p] = s; break;}
}
}
/* Rebuild the point strata on the receiver */
ierr = PetscCalloc1((*labelNew)->numStrata,&(*labelNew)->stratumSizes);CHKERRQ(ierr);
ierr = PetscSectionGetChart(leafSection, &pStart, &pEnd);CHKERRQ(ierr);
for (p=pStart; p<pEnd; p++) {
ierr = PetscSectionGetDof(leafSection, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(leafSection, p, &offset);CHKERRQ(ierr);
for (s=0; s<dof; s++) {
(*labelNew)->stratumSizes[leafStrata[offset+s]]++;
}
}
ierr = PetscCalloc1((*labelNew)->numStrata,&(*labelNew)->ht);CHKERRQ(ierr);
ierr = PetscMalloc1((*labelNew)->numStrata,&(*labelNew)->points);CHKERRQ(ierr);
ierr = PetscMalloc1((*labelNew)->numStrata,&points);CHKERRQ(ierr);
for (s = 0; s < (*labelNew)->numStrata; ++s) {
PetscHashICreate((*labelNew)->ht[s]);
ierr = PetscMalloc1((*labelNew)->stratumSizes[s], &(points[s]));CHKERRQ(ierr);
}
/* Insert points into new strata */
ierr = PetscCalloc1((*labelNew)->numStrata, &strataIdx);CHKERRQ(ierr);
ierr = PetscSectionGetChart(leafSection, &pStart, &pEnd);CHKERRQ(ierr);
for (p=pStart; p<pEnd; p++) {
ierr = PetscSectionGetDof(leafSection, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(leafSection, p, &offset);CHKERRQ(ierr);
for (s=0; s<dof; s++) {
stratum = leafStrata[offset+s];
points[stratum][strataIdx[stratum]++] = p;
}
}
for (s = 0; s < (*labelNew)->numStrata; s++) {
ierr = ISCreateGeneral(PETSC_COMM_SELF,(*labelNew)->stratumSizes[s],&(points[s][0]),PETSC_OWN_POINTER,&((*labelNew)->points[s]));CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)((*labelNew)->points[s]),"indices");CHKERRQ(ierr);
}
ierr = PetscFree(points);CHKERRQ(ierr);
PetscHashIDestroy(stratumHash);
ierr = PetscFree(leafStrata);CHKERRQ(ierr);
ierr = PetscFree(strataIdx);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&leafSection);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMLabelGather - Gather all label values from leafs into roots
Input Parameters:
+ label - the DMLabel
. point - the Star Forest point communication map
Input Parameters:
+ label - the new DMLabel with localised leaf values
Level: developer
Note: This is the inverse operation to DMLabelDistribute.
.seealso: DMLabelDistribute()
@*/
PetscErrorCode DMLabelGather(DMLabel label, PetscSF sf, DMLabel *labelNew)
{
MPI_Comm comm;
PetscSection rootSection;
PetscSF sfLabel;
PetscSFNode *rootPoints, *leafPoints;
PetscInt p, s, d, nroots, nleaves, nmultiroots, idx, dof, offset;
const PetscInt *rootDegree, *ilocal;
PetscInt *rootStrata;
char *name;
PetscInt nameSize;
size_t len = 0;
PetscMPIInt rank, numProcs;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)sf, &comm);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
/* Bcast name */
if (!rank) {ierr = PetscStrlen(label->name, &len);CHKERRQ(ierr);}
nameSize = len;
ierr = MPI_Bcast(&nameSize, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
ierr = PetscMalloc1(nameSize+1, &name);CHKERRQ(ierr);
if (!rank) {ierr = PetscMemcpy(name, label->name, nameSize+1);CHKERRQ(ierr);}
ierr = MPI_Bcast(name, nameSize+1, MPI_CHAR, 0, comm);CHKERRQ(ierr);
ierr = DMLabelCreate(name, labelNew);CHKERRQ(ierr);
ierr = PetscFree(name);CHKERRQ(ierr);
/* Gather rank/index pairs of leaves into local roots to build
an inverse, multi-rooted SF. Note that this ignores local leaf
indexing due to the use of the multiSF in PetscSFGather. */
ierr = PetscSFGetGraph(sf, &nroots, &nleaves, &ilocal, NULL);CHKERRQ(ierr);
ierr = PetscMalloc1(nroots, &leafPoints);CHKERRQ(ierr);
for (p = 0; p < nroots; ++p) leafPoints[p].rank = leafPoints[p].index = -1;
for (p = 0; p < nleaves; p++) {
leafPoints[ilocal[p]].index = ilocal[p];
leafPoints[ilocal[p]].rank = rank;
}
ierr = PetscSFComputeDegreeBegin(sf, &rootDegree);CHKERRQ(ierr);
ierr = PetscSFComputeDegreeEnd(sf, &rootDegree);CHKERRQ(ierr);
for (p = 0, nmultiroots = 0; p < nroots; ++p) nmultiroots += rootDegree[p];
ierr = PetscMalloc1(nmultiroots, &rootPoints);CHKERRQ(ierr);
ierr = PetscSFGatherBegin(sf, MPIU_2INT, leafPoints, rootPoints);CHKERRQ(ierr);
ierr = PetscSFGatherEnd(sf, MPIU_2INT, leafPoints, rootPoints);CHKERRQ(ierr);
ierr = PetscSFCreate(comm,& sfLabel);CHKERRQ(ierr);
ierr = PetscSFSetGraph(sfLabel, nroots, nmultiroots, NULL, PETSC_OWN_POINTER, rootPoints, PETSC_OWN_POINTER);CHKERRQ(ierr);
/* Migrate label over inverted SF to pull stratum values at leaves into roots. */
ierr = DMLabelDistribute_Internal(label, sfLabel, &rootSection, &rootStrata);CHKERRQ(ierr);
/* Rebuild the point strata on the receiver */
for (p = 0, idx = 0; p < nroots; p++) {
for (d = 0; d < rootDegree[p]; d++) {
ierr = PetscSectionGetDof(rootSection, idx+d, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(rootSection, idx+d, &offset);CHKERRQ(ierr);
for (s = 0; s < dof; s++) {ierr = DMLabelSetValue(*labelNew, p, rootStrata[offset+s]);CHKERRQ(ierr);}
}
idx += rootDegree[p];
}
ierr = PetscFree(leafPoints);CHKERRQ(ierr);
ierr = PetscFree(rootStrata);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&rootSection);CHKERRQ(ierr);
ierr = PetscSFDestroy(&sfLabel);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
DM dm, dmDist = NULL;
Vec u;
PetscSection section;
PetscViewer viewer;
PetscInt dim = 2, numFields, numBC, i;
PetscInt numComp[3];
PetscInt numDof[12];
PetscInt bcField[1];
IS bcPointIS[1];
PetscBool interpolate = PETSC_TRUE;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL, "-dim", &dim, NULL);CHKERRQ(ierr);
/* Create a mesh */
ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD, dim, interpolate, &dm);CHKERRQ(ierr);
/* Distribute mesh over processes */
ierr = DMPlexDistribute(dm, 0, NULL, &dmDist);CHKERRQ(ierr);
if (dmDist) {ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = dmDist;}
/* Create a scalar field u, a vector field v, and a surface vector field w */
numFields = 3;
numComp[0] = 1;
numComp[1] = dim;
numComp[2] = dim-1;
for (i = 0; i < numFields*(dim+1); ++i) numDof[i] = 0;
/* Let u be defined on vertices */
numDof[0*(dim+1)+0] = 1;
/* Let v be defined on cells */
numDof[1*(dim+1)+dim] = dim;
/* Let v be defined on faces */
numDof[2*(dim+1)+dim-1] = dim-1;
/* Setup boundary conditions */
numBC = 1;
/* Prescribe a Dirichlet condition on u on the boundary
Label "marker" is made by the mesh creation routine */
bcField[0] = 0;
ierr = DMPlexGetStratumIS(dm, "marker", 1, &bcPointIS[0]);CHKERRQ(ierr);
/* Create a PetscSection with this data layout */
ierr = DMPlexCreateSection(dm, dim, numFields, numComp, numDof, numBC, bcField, bcPointIS, NULL, §ion);CHKERRQ(ierr);
ierr = ISDestroy(&bcPointIS[0]);CHKERRQ(ierr);
/* Name the Field variables */
ierr = PetscSectionSetFieldName(section, 0, "u");CHKERRQ(ierr);
ierr = PetscSectionSetFieldName(section, 1, "v");CHKERRQ(ierr);
ierr = PetscSectionSetFieldName(section, 2, "w");CHKERRQ(ierr);
ierr = PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* Tell the DM to use this data layout */
ierr = DMSetDefaultSection(dm, section);CHKERRQ(ierr);
/* Create a Vec with this layout and view it */
ierr = DMGetGlobalVector(dm, &u);CHKERRQ(ierr);
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "sol.vtk");CHKERRQ(ierr);
ierr = VecView(u, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dm, &u);CHKERRQ(ierr);
/* Cleanup */
ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
/* This interpolates the PointSF in parallel following local interpolation */
static PetscErrorCode DMPlexInterpolatePointSF(DM dm, PetscSF pointSF, PetscInt depth)
{
PetscMPIInt numProcs, rank;
PetscInt p, c, d, dof, offset;
PetscInt numLeaves, numRoots, candidatesSize, candidatesRemoteSize;
const PetscInt *localPoints;
const PetscSFNode *remotePoints;
PetscSFNode *candidates, *candidatesRemote, *claims;
PetscSection candidateSection, candidateSectionRemote, claimSection;
PetscHashI leafhash;
PetscHashIJ roothash;
PetscHashIJKey key;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &numProcs);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr);
ierr = PetscSFGetGraph(pointSF, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr);
if (numProcs < 2 || numRoots < 0) PetscFunctionReturn(0);
/* Build hashes of points in the SF for efficient lookup */
PetscHashICreate(leafhash);
PetscHashIJCreate(&roothash);
ierr = PetscHashIJSetMultivalued(roothash, PETSC_FALSE);CHKERRQ(ierr);
for (p = 0; p < numLeaves; ++p) {
PetscHashIAdd(leafhash, localPoints[p], p);
key.i = remotePoints[p].index; key.j = remotePoints[p].rank;
PetscHashIJAdd(roothash, key, p);
}
/* Build a section / SFNode array of candidate points in the single-level adjacency of leaves,
where each candidate is defined by the root entry for the other vertex that defines the edge. */
ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), &candidateSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(candidateSection, 0, numRoots);CHKERRQ(ierr);
{
PetscInt leaf, root, idx, a, *adj = NULL;
for (p = 0; p < numLeaves; ++p) {
PetscInt adjSize = PETSC_DETERMINE;
ierr = DMPlexGetAdjacency_Internal(dm, localPoints[p], PETSC_FALSE, PETSC_FALSE, PETSC_FALSE, &adjSize, &adj);CHKERRQ(ierr);
for (a = 0; a < adjSize; ++a) {
PetscHashIMap(leafhash, adj[a], leaf);
if (leaf >= 0) {ierr = PetscSectionAddDof(candidateSection, localPoints[p], 1);CHKERRQ(ierr);}
}
}
ierr = PetscSectionSetUp(candidateSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(candidateSection, &candidatesSize);CHKERRQ(ierr);
ierr = PetscMalloc1(candidatesSize, &candidates);CHKERRQ(ierr);
for (p = 0; p < numLeaves; ++p) {
PetscInt adjSize = PETSC_DETERMINE;
ierr = PetscSectionGetOffset(candidateSection, localPoints[p], &offset);CHKERRQ(ierr);
ierr = DMPlexGetAdjacency_Internal(dm, localPoints[p], PETSC_FALSE, PETSC_FALSE, PETSC_FALSE, &adjSize, &adj);CHKERRQ(ierr);
for (idx = 0, a = 0; a < adjSize; ++a) {
PetscHashIMap(leafhash, adj[a], root);
if (root >= 0) candidates[offset+idx++] = remotePoints[root];
}
}
ierr = PetscFree(adj);CHKERRQ(ierr);
}
/* Gather candidate section / array pair into the root partition via inverse(multi(pointSF)). */
{
PetscSF sfMulti, sfInverse, sfCandidates;
PetscInt *remoteOffsets;
ierr = PetscSFGetMultiSF(pointSF, &sfMulti);CHKERRQ(ierr);
ierr = PetscSFCreateInverseSF(sfMulti, &sfInverse);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), &candidateSectionRemote);CHKERRQ(ierr);
ierr = PetscSFDistributeSection(sfInverse, candidateSection, &remoteOffsets, candidateSectionRemote);CHKERRQ(ierr);
ierr = PetscSFCreateSectionSF(sfInverse, candidateSection, remoteOffsets, candidateSectionRemote, &sfCandidates);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(candidateSectionRemote, &candidatesRemoteSize);CHKERRQ(ierr);
ierr = PetscMalloc1(candidatesRemoteSize, &candidatesRemote);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(sfCandidates, MPIU_2INT, candidates, candidatesRemote);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(sfCandidates, MPIU_2INT, candidates, candidatesRemote);CHKERRQ(ierr);
ierr = PetscSFDestroy(&sfInverse);CHKERRQ(ierr);
ierr = PetscSFDestroy(&sfCandidates);CHKERRQ(ierr);
ierr = PetscFree(remoteOffsets);CHKERRQ(ierr);
}
/* Walk local roots and check for each remote candidate whether we know all required points,
either from owning it or having a root entry in the point SF. If we do we place a claim
by replacing the vertex number with our edge ID. */
{
PetscInt idx, root, joinSize, vertices[2];
const PetscInt *rootdegree, *join = NULL;
ierr = PetscSFComputeDegreeBegin(pointSF, &rootdegree);CHKERRQ(ierr);
ierr = PetscSFComputeDegreeEnd(pointSF, &rootdegree);CHKERRQ(ierr);
/* Loop remote edge connections and put in a claim if both vertices are known */
for (idx = 0, p = 0; p < numRoots; ++p) {
for (d = 0; d < rootdegree[p]; ++d) {
ierr = PetscSectionGetDof(candidateSectionRemote, idx, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(candidateSectionRemote, idx, &offset);CHKERRQ(ierr);
for (c = 0; c < dof; ++c) {
/* We own both vertices, so we claim the edge by replacing vertex with edge */
if (candidatesRemote[offset+c].rank == rank) {
vertices[0] = p; vertices[1] = candidatesRemote[offset+c].index;
ierr = DMPlexGetJoin(dm, 2, vertices, &joinSize, &join);CHKERRQ(ierr);
if (joinSize == 1) candidatesRemote[offset+c].index = join[0];
ierr = DMPlexRestoreJoin(dm, 2, vertices, &joinSize, &join);CHKERRQ(ierr);
continue;
}
/* If we own one vertex and share a root with the other, we claim it */
key.i = candidatesRemote[offset+c].index; key.j = candidatesRemote[offset+c].rank;
PetscHashIJGet(roothash, key, &root);
if (root >= 0) {
vertices[0] = p; vertices[1] = localPoints[root];
ierr = DMPlexGetJoin(dm, 2, vertices, &joinSize, &join);CHKERRQ(ierr);
if (joinSize == 1) {
candidatesRemote[offset+c].index = join[0];
candidatesRemote[offset+c].rank = rank;
}
ierr = DMPlexRestoreJoin(dm, 2, vertices, &joinSize, &join);CHKERRQ(ierr);
}
}
idx++;
}
}
}
/* Push claims back to receiver via the MultiSF and derive new pointSF mapping on receiver */
{
PetscSF sfMulti, sfClaims, sfPointNew;
PetscHashI claimshash;
PetscInt size, pStart, pEnd, root, joinSize, numLocalNew;
PetscInt *remoteOffsets, *localPointsNew, vertices[2];
const PetscInt *join = NULL;
PetscSFNode *remotePointsNew;
ierr = PetscSFGetMultiSF(pointSF, &sfMulti);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), &claimSection);CHKERRQ(ierr);
ierr = PetscSFDistributeSection(sfMulti, candidateSectionRemote, &remoteOffsets, claimSection);CHKERRQ(ierr);
ierr = PetscSFCreateSectionSF(sfMulti, candidateSectionRemote, remoteOffsets, claimSection, &sfClaims);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(claimSection, &size);CHKERRQ(ierr);
ierr = PetscMalloc1(size, &claims);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(sfClaims, MPIU_2INT, candidatesRemote, claims);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(sfClaims, MPIU_2INT, candidatesRemote, claims);CHKERRQ(ierr);
ierr = PetscSFDestroy(&sfClaims);CHKERRQ(ierr);
ierr = PetscFree(remoteOffsets);CHKERRQ(ierr);
/* Walk the original section of local supports and add an SF entry for each updated item */
PetscHashICreate(claimshash);
for (p = 0; p < numRoots; ++p) {
ierr = PetscSectionGetDof(candidateSection, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(candidateSection, p, &offset);CHKERRQ(ierr);
for (d = 0; d < dof; ++d) {
if (candidates[offset+d].index != claims[offset+d].index) {
key.i = candidates[offset+d].index; key.j = candidates[offset+d].rank;
PetscHashIJGet(roothash, key, &root);
if (root >= 0) {
vertices[0] = p; vertices[1] = localPoints[root];
ierr = DMPlexGetJoin(dm, 2, vertices, &joinSize, &join);CHKERRQ(ierr);
if (joinSize == 1) PetscHashIAdd(claimshash, join[0], offset+d);
ierr = DMPlexRestoreJoin(dm, 2, vertices, &joinSize, &join);CHKERRQ(ierr);
}
}
}
}
/* Create new pointSF from hashed claims */
PetscHashISize(claimshash, numLocalNew);
ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr);
ierr = PetscMalloc1(numLeaves + numLocalNew, &localPointsNew);CHKERRQ(ierr);
ierr = PetscMalloc1(numLeaves + numLocalNew, &remotePointsNew);CHKERRQ(ierr);
for (p = 0; p < numLeaves; ++p) {
localPointsNew[p] = localPoints[p];
remotePointsNew[p].index = remotePoints[p].index;
remotePointsNew[p].rank = remotePoints[p].rank;
}
p = numLeaves; ierr = PetscHashIGetKeys(claimshash, &p, localPointsNew);CHKERRQ(ierr);
for (p = numLeaves; p < numLeaves + numLocalNew; ++p) {
PetscHashIMap(claimshash, localPointsNew[p], offset);
remotePointsNew[p] = claims[offset];
}
ierr = PetscSFCreate(PetscObjectComm((PetscObject) dm), &sfPointNew);CHKERRQ(ierr);
ierr = PetscSFSetGraph(sfPointNew, pEnd-pStart, numLeaves+numLocalNew, localPointsNew, PETSC_OWN_POINTER, remotePointsNew, PETSC_OWN_POINTER);CHKERRQ(ierr);
ierr = DMSetPointSF(dm, sfPointNew);CHKERRQ(ierr);
ierr = PetscSFDestroy(&sfPointNew);CHKERRQ(ierr);
PetscHashIDestroy(claimshash);
}
PetscHashIDestroy(leafhash);
ierr = PetscHashIJDestroy(&roothash);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&candidateSection);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&candidateSectionRemote);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&claimSection);CHKERRQ(ierr);
ierr = PetscFree(candidates);CHKERRQ(ierr);
ierr = PetscFree(candidatesRemote);CHKERRQ(ierr);
ierr = PetscFree(claims);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* get adjacencies due to point-to-point constraints that can't be found with DMPlexGetAdjacency() */
static PetscErrorCode DMPlexComputeAnchorAdjacencies(DM dm, PetscSection section, PetscSection sectionGlobal, PetscSection *anchorSectionAdj, PetscInt *anchorAdj[])
{
PetscInt pStart, pEnd;
PetscSection adjSec, aSec;
IS aIS;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscSectionCreate(PetscObjectComm((PetscObject)section),&adjSec);CHKERRQ(ierr);
ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr);
ierr = PetscSectionSetChart(adjSec,pStart,pEnd);CHKERRQ(ierr);
ierr = DMPlexGetAnchors(dm,&aSec,&aIS);CHKERRQ(ierr);
if (aSec) {
const PetscInt *anchors;
PetscInt p, q, a, aSize, *offsets, aStart, aEnd, *inverse, iSize, *adj, adjSize;
PetscInt *tmpAdjP = NULL, *tmpAdjQ = NULL;
PetscSection inverseSec;
/* invert the constraint-to-anchor map */
ierr = PetscSectionCreate(PetscObjectComm((PetscObject)aSec),&inverseSec);CHKERRQ(ierr);
ierr = PetscSectionSetChart(inverseSec,pStart,pEnd);CHKERRQ(ierr);
ierr = ISGetLocalSize(aIS, &aSize);CHKERRQ(ierr);
ierr = ISGetIndices(aIS, &anchors);CHKERRQ(ierr);
for (p = 0; p < aSize; p++) {
PetscInt a = anchors[p];
ierr = PetscSectionAddDof(inverseSec,a,1);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(inverseSec);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(inverseSec,&iSize);CHKERRQ(ierr);
ierr = PetscMalloc1(iSize,&inverse);CHKERRQ(ierr);
ierr = PetscCalloc1(pEnd-pStart,&offsets);CHKERRQ(ierr);
ierr = PetscSectionGetChart(aSec,&aStart,&aEnd);CHKERRQ(ierr);
for (p = aStart; p < aEnd; p++) {
PetscInt dof, off;
ierr = PetscSectionGetDof(aSec, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(aSec, p, &off);CHKERRQ(ierr);
for (q = 0; q < dof; q++) {
PetscInt iOff;
a = anchors[off + q];
ierr = PetscSectionGetOffset(inverseSec, a, &iOff);CHKERRQ(ierr);
inverse[iOff + offsets[a-pStart]++] = p;
}
}
ierr = ISRestoreIndices(aIS, &anchors);CHKERRQ(ierr);
ierr = PetscFree(offsets);CHKERRQ(ierr);
/* construct anchorAdj and adjSec
*
* loop over anchors:
* construct anchor adjacency
* loop over constrained:
* construct constrained adjacency
* if not in anchor adjacency, add to dofs
* setup adjSec, allocate anchorAdj
* loop over anchors:
* construct anchor adjacency
* loop over constrained:
* construct constrained adjacency
* if not in anchor adjacency
* if not already in list, put in list
* sort, unique, reduce dof count
* optional: compactify
*/
for (p = pStart; p < pEnd; p++) {
PetscInt iDof, iOff, i, r, s, numAdjP = PETSC_DETERMINE;
ierr = PetscSectionGetDof(inverseSec,p,&iDof);CHKERRQ(ierr);
if (!iDof) continue;
ierr = PetscSectionGetOffset(inverseSec,p,&iOff);CHKERRQ(ierr);
ierr = DMPlexGetAdjacency(dm,p,&numAdjP,&tmpAdjP);CHKERRQ(ierr);
for (i = 0; i < iDof; i++) {
PetscInt iNew = 0, qAdj, qAdjDof, qAdjCDof, numAdjQ = PETSC_DETERMINE;
q = inverse[iOff + i];
ierr = DMPlexGetAdjacency(dm,q,&numAdjQ,&tmpAdjQ);CHKERRQ(ierr);
for (r = 0; r < numAdjQ; r++) {
qAdj = tmpAdjQ[r];
if ((qAdj < pStart) || (qAdj >= pEnd)) continue;
for (s = 0; s < numAdjP; s++) {
if (qAdj == tmpAdjP[s]) break;
}
if (s < numAdjP) continue;
ierr = PetscSectionGetDof(section,qAdj,&qAdjDof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section,qAdj,&qAdjCDof);CHKERRQ(ierr);
iNew += qAdjDof - qAdjCDof;
}
ierr = PetscSectionAddDof(adjSec,p,iNew);CHKERRQ(ierr);
}
}
ierr = PetscSectionSetUp(adjSec);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(adjSec,&adjSize);CHKERRQ(ierr);
ierr = PetscMalloc1(adjSize,&adj);CHKERRQ(ierr);
for (p = pStart; p < pEnd; p++) {
PetscInt iDof, iOff, i, r, s, aOff, aOffOrig, aDof, numAdjP = PETSC_DETERMINE;
ierr = PetscSectionGetDof(inverseSec,p,&iDof);CHKERRQ(ierr);
if (!iDof) continue;
ierr = PetscSectionGetOffset(inverseSec,p,&iOff);CHKERRQ(ierr);
ierr = DMPlexGetAdjacency(dm,p,&numAdjP,&tmpAdjP);CHKERRQ(ierr);
ierr = PetscSectionGetDof(adjSec,p,&aDof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(adjSec,p,&aOff);CHKERRQ(ierr);
aOffOrig = aOff;
for (i = 0; i < iDof; i++) {
PetscInt qAdj, qAdjDof, qAdjCDof, qAdjOff, nd, numAdjQ = PETSC_DETERMINE;
q = inverse[iOff + i];
ierr = DMPlexGetAdjacency(dm,q,&numAdjQ,&tmpAdjQ);CHKERRQ(ierr);
for (r = 0; r < numAdjQ; r++) {
qAdj = tmpAdjQ[r];
if ((qAdj < pStart) || (qAdj >= pEnd)) continue;
for (s = 0; s < numAdjP; s++) {
if (qAdj == tmpAdjP[s]) break;
}
if (s < numAdjP) continue;
ierr = PetscSectionGetDof(section,qAdj,&qAdjDof);CHKERRQ(ierr);
ierr = PetscSectionGetConstraintDof(section,qAdj,&qAdjCDof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(sectionGlobal,qAdj,&qAdjOff);CHKERRQ(ierr);
for (nd = 0; nd < qAdjDof-qAdjCDof; ++nd) {
adj[aOff++] = (qAdjOff < 0 ? -(qAdjOff+1) : qAdjOff) + nd;
}
}
}
ierr = PetscSortRemoveDupsInt(&aDof,&adj[aOffOrig]);CHKERRQ(ierr);
ierr = PetscSectionSetDof(adjSec,p,aDof);CHKERRQ(ierr);
}
*anchorAdj = adj;
/* clean up */
ierr = PetscSectionDestroy(&inverseSec);CHKERRQ(ierr);
ierr = PetscFree(inverse);CHKERRQ(ierr);
ierr = PetscFree(tmpAdjP);CHKERRQ(ierr);
ierr = PetscFree(tmpAdjQ);CHKERRQ(ierr);
}
else {
*anchorAdj = NULL;
ierr = PetscSectionSetUp(adjSec);CHKERRQ(ierr);
}
*anchorSectionAdj = adjSec;
PetscFunctionReturn(0);
}
//! Help PETSc identify the coarser DM dmc given the fine DM dmf
PetscErrorCode libmesh_petsc_DMCoarsen(DM dmf, MPI_Comm /*comm*/, DM * dmc)
{
libmesh_assert(dmc);
libmesh_assert(dmf);
PetscErrorCode ierr;
// Extract our context from the incoming dmf
void * ctx_f = nullptr;
ierr = DMShellGetContext(dmf, &ctx_f);LIBMESH_CHKERR(ierr);
libmesh_assert(ctx_f);
PetscDMContext * p_ctx = static_cast<PetscDMContext*>(ctx_f);
// First, ensure that there exists a coarse DM that we want to
// set. There ought to be as we created it while walking the
// hierarchy.
libmesh_assert(p_ctx->coarser_dm);
libmesh_assert(*(p_ctx->coarser_dm));
// In situations using fieldsplit we need to (potentially)
// provide a coarser DM which only has the relevant subfields in
// it. Since we create global DMs for each mesh level, we need
// to extract the section from the DM, and check the number of
// fields. When less than all the fields are used, we need to
// create the proper subsections.
// Get the number of fields and their names from the incomming
// fine DM and the global reference DM
PetscInt nfieldsf, nfieldsg;
char ** fieldnamesf;
char ** fieldnamesg;
libmesh_assert(p_ctx->global_dm);
DM * globaldm = p_ctx->global_dm;
ierr = DMCreateFieldIS(dmf, &nfieldsf, &fieldnamesf, nullptr);
LIBMESH_CHKERR(ierr);
ierr = DMCreateFieldIS(*globaldm, &nfieldsg, &fieldnamesg, nullptr);
LIBMESH_CHKERR(ierr);
// If the probed number of fields is less than the number of
// global fields, this amounts to PETSc 'indicating' to us we
// are doing FS. So, we must create subsections for the coarser
// DMs.
if ( nfieldsf < nfieldsg )
{
PetscSection section;
PetscSection subsection;
std::vector<PetscInt> subfields(nfieldsf); // extracted fields
// First, get the section from the coarse DM
#if PETSC_VERSION_LESS_THAN(3,10,0)
ierr = DMGetDefaultSection(*(p_ctx->coarser_dm), §ion);
#else
ierr = DMGetSection(*(p_ctx->coarser_dm), §ion);
#endif
LIBMESH_CHKERR(ierr);
// Now, match fine grid DM field names to their global DM
// counterparts. Since PETSc can internally reassign field
// numbering under a fieldsplit, we must extract
// subsections via the field names. This is admittedly
// gross, but c'est la vie.
for (int i = 0; i < nfieldsf ; i++)
{
for (int j = 0; j < nfieldsg ;j++)
if ( strcmp( fieldnamesg[j], fieldnamesf[i] ) == 0 )
subfields[i] = j;
}
// Next, for the found fields we now make a subsection and set it for the coarser DM
ierr = PetscSectionCreateSubsection(section, nfieldsf, subfields.data(), &subsection);
LIBMESH_CHKERR(ierr);
#if PETSC_VERSION_LESS_THAN(3,10,0)
ierr = DMSetDefaultSection(*(p_ctx->coarser_dm) , subsection);
#else
ierr = DMSetSection(*(p_ctx->coarser_dm) , subsection);
#endif
LIBMESH_CHKERR(ierr);
ierr = PetscSectionDestroy(&subsection);
LIBMESH_CHKERR(ierr);
}
// Finally, set the coarser DM
*(dmc) = *(p_ctx->coarser_dm);
return 0;
}
/* Distribute cones
- Partitioning: input partition point map and naive sf, output sf with inverse of map, distribute points
- Distribute section: input current sf, communicate sizes and offsets, output local section and offsets (only use for new sf)
- Create SF for values: input current sf and offsets, output new sf
- Distribute values: input new sf, communicate values
*/
PetscErrorCode DistributeMesh(DM dm, AppCtx *user, PetscSF *pointSF, DM *parallelDM)
{
MPI_Comm comm = ((PetscObject) dm)->comm;
const PetscInt height = 0;
PetscInt dim, numRemoteRanks;
IS cellPart, part;
PetscSection cellPartSection, partSection;
PetscSFNode *remoteRanks;
PetscSF partSF;
ISLocalToGlobalMapping renumbering;
PetscSF coneSF;
PetscSection originalConeSection, newConeSection;
PetscInt *remoteOffsets, newConesSize;
PetscInt *cones, *newCones;
PetscMPIInt numProcs, rank, p;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = DMMeshGetDimension(dm, &dim);CHKERRQ(ierr);
/* Create cell partition - We need to rewrite to use IS, use the MatPartition stuff */
ierr = DMMeshCreatePartition(dm, &cellPartSection, &cellPart, height);CHKERRQ(ierr);
/* Create SF assuming a serial partition for all processes: Could check for IS length here */
if (!rank) {
numRemoteRanks = numProcs;
} else {
numRemoteRanks = 0;
}
ierr = PetscMalloc(numRemoteRanks * sizeof(PetscSFNode), &remoteRanks);CHKERRQ(ierr);
for(p = 0; p < numRemoteRanks; ++p) {
remoteRanks[p].rank = p;
remoteRanks[p].index = 0;
}
ierr = PetscSFCreate(comm, &partSF);CHKERRQ(ierr);
ierr = PetscSFSetGraph(partSF, 1, numRemoteRanks, PETSC_NULL, PETSC_OWN_POINTER, remoteRanks, PETSC_OWN_POINTER);CHKERRQ(ierr);
/* Debugging */
ierr = PetscPrintf(comm, "Cell Partition:\n");CHKERRQ(ierr);
ierr = PetscSectionView(cellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(cellPart, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscSFView(partSF, PETSC_NULL);CHKERRQ(ierr);
/* Close the partition over the mesh */
ierr = DMMeshCreatePartitionClosure(dm, cellPartSection, cellPart, &partSection, &part);CHKERRQ(ierr);
ierr = ISDestroy(&cellPart);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr);
/* Create new mesh */
ierr = DMMeshCreate(comm, parallelDM);CHKERRQ(ierr);
ierr = DMMeshSetDimension(*parallelDM, dim);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) *parallelDM, "Parallel Mesh");CHKERRQ(ierr);
/* Distribute sieve points and the global point numbering (replaces creating remote bases) */
ierr = PetscSFConvertPartition(partSF, partSection, part, &renumbering, pointSF);CHKERRQ(ierr);
/* Debugging */
ierr = PetscPrintf(comm, "Point Partition:\n");CHKERRQ(ierr);
ierr = PetscSectionView(partSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(part, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscSFView(*pointSF, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Point Renumbering after partition:\n");CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingView(renumbering, PETSC_NULL);CHKERRQ(ierr);
/* Cleanup */
ierr = PetscSFDestroy(&partSF);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&partSection);CHKERRQ(ierr);
ierr = ISDestroy(&part);CHKERRQ(ierr);
/* Distribute cone section */
ierr = DMMeshGetConeSection(dm, &originalConeSection);CHKERRQ(ierr);
ierr = DMMeshGetConeSection(*parallelDM, &newConeSection);CHKERRQ(ierr);
ierr = PetscSFDistributeSection(*pointSF, originalConeSection, &remoteOffsets, newConeSection);CHKERRQ(ierr);
ierr = DMMeshSetUp(*parallelDM);CHKERRQ(ierr);
/* Communicate and renumber cones */
ierr = PetscSFCreateSectionSF(*pointSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);CHKERRQ(ierr);
ierr = DMMeshGetCones(dm, &cones);CHKERRQ(ierr);
ierr = DMMeshGetCones(*parallelDM, &newCones);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(newConeSection, &newConesSize);CHKERRQ(ierr);
ierr = ISGlobalToLocalMappingApply(renumbering, IS_GTOLM_MASK, newConesSize, newCones, PETSC_NULL, newCones);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingDestroy(&renumbering);CHKERRQ(ierr);
/* Debugging */
ierr = PetscPrintf(comm, "Serial Cone Section:\n");CHKERRQ(ierr);
ierr = PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Parallel Cone Section:\n");CHKERRQ(ierr);
ierr = PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscSFView(coneSF, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscSFDestroy(&coneSF);CHKERRQ(ierr);
/* Create supports and stratify sieve */
ierr = DMMeshSymmetrize(*parallelDM);CHKERRQ(ierr);
ierr = DMMeshStratify(*parallelDM);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
DMPlexDistribute - Distributes the mesh and any associated sections.
Not Collective
Input Parameter:
+ dm - The original DMPlex object
. partitioner - The partitioning package, or NULL for the default
- overlap - The overlap of partitions, 0 is the default
Output Parameter:
+ sf - The PetscSF used for point distribution
- parallelMesh - The distributed DMPlex object, or NULL
Note: If the mesh was not distributed, the return value is NULL.
The user can control the definition of adjacency for the mesh using DMPlexGetAdjacencyUseCone() and
DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function
representation on the mesh.
Level: intermediate
.keywords: mesh, elements
.seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure()
@*/
PetscErrorCode DMPlexDistribute(DM dm, const char partitioner[], PetscInt overlap, PetscSF *sf, DM *dmParallel)
{
DM_Plex *mesh = (DM_Plex*) dm->data, *pmesh;
MPI_Comm comm;
const PetscInt height = 0;
PetscInt dim, numRemoteRanks;
IS origCellPart, origPart, cellPart, part;
PetscSection origCellPartSection, origPartSection, cellPartSection, partSection;
PetscSFNode *remoteRanks;
PetscSF partSF, pointSF, coneSF;
ISLocalToGlobalMapping renumbering;
PetscSection originalConeSection, newConeSection;
PetscInt *remoteOffsets;
PetscInt *cones, *newCones, newConesSize;
PetscBool flg;
PetscMPIInt rank, numProcs, p;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
if (sf) PetscValidPointer(sf,4);
PetscValidPointer(dmParallel,5);
ierr = PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr);
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
*dmParallel = NULL;
if (numProcs == 1) PetscFunctionReturn(0);
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
/* Create cell partition - We need to rewrite to use IS, use the MatPartition stuff */
ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr);
if (overlap > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Overlap > 1 not yet implemented");
ierr = DMPlexCreatePartition(dm, partitioner, height, overlap > 0 ? PETSC_TRUE : PETSC_FALSE, &cellPartSection, &cellPart, &origCellPartSection, &origCellPart);CHKERRQ(ierr);
/* Create SF assuming a serial partition for all processes: Could check for IS length here */
if (!rank) numRemoteRanks = numProcs;
else numRemoteRanks = 0;
ierr = PetscMalloc1(numRemoteRanks, &remoteRanks);CHKERRQ(ierr);
for (p = 0; p < numRemoteRanks; ++p) {
remoteRanks[p].rank = p;
remoteRanks[p].index = 0;
}
ierr = PetscSFCreate(comm, &partSF);CHKERRQ(ierr);
ierr = PetscSFSetGraph(partSF, 1, numRemoteRanks, NULL, PETSC_OWN_POINTER, remoteRanks, PETSC_OWN_POINTER);CHKERRQ(ierr);
ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(comm, "Cell Partition:\n");CHKERRQ(ierr);
ierr = PetscSectionView(cellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(cellPart, NULL);CHKERRQ(ierr);
if (origCellPart) {
ierr = PetscPrintf(comm, "Original Cell Partition:\n");CHKERRQ(ierr);
ierr = PetscSectionView(origCellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(origCellPart, NULL);CHKERRQ(ierr);
}
ierr = PetscSFView(partSF, NULL);CHKERRQ(ierr);
}
/* Close the partition over the mesh */
ierr = DMPlexCreatePartitionClosure(dm, cellPartSection, cellPart, &partSection, &part);CHKERRQ(ierr);
ierr = ISDestroy(&cellPart);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr);
/* Create new mesh */
ierr = DMPlexCreate(comm, dmParallel);CHKERRQ(ierr);
ierr = DMPlexSetDimension(*dmParallel, dim);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");CHKERRQ(ierr);
pmesh = (DM_Plex*) (*dmParallel)->data;
/* Distribute sieve points and the global point numbering (replaces creating remote bases) */
ierr = PetscSFConvertPartition(partSF, partSection, part, &renumbering, &pointSF);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(comm, "Point Partition:\n");CHKERRQ(ierr);
ierr = PetscSectionView(partSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(part, NULL);CHKERRQ(ierr);
ierr = PetscSFView(pointSF, NULL);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Point Renumbering after partition:\n");CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingView(renumbering, NULL);CHKERRQ(ierr);
}
ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr);
ierr = PetscLogEventBegin(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr);
/* Distribute cone section */
ierr = DMPlexGetConeSection(dm, &originalConeSection);CHKERRQ(ierr);
ierr = DMPlexGetConeSection(*dmParallel, &newConeSection);CHKERRQ(ierr);
ierr = PetscSFDistributeSection(pointSF, originalConeSection, &remoteOffsets, newConeSection);CHKERRQ(ierr);
ierr = DMSetUp(*dmParallel);CHKERRQ(ierr);
{
PetscInt pStart, pEnd, p;
ierr = PetscSectionGetChart(newConeSection, &pStart, &pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt coneSize;
ierr = PetscSectionGetDof(newConeSection, p, &coneSize);CHKERRQ(ierr);
pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize);
}
}
/* Communicate and renumber cones */
ierr = PetscSFCreateSectionSF(pointSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);CHKERRQ(ierr);
ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr);
ierr = DMPlexGetCones(*dmParallel, &newCones);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(newConeSection, &newConesSize);CHKERRQ(ierr);
ierr = ISGlobalToLocalMappingApply(renumbering, IS_GTOLM_MASK, newConesSize, newCones, NULL, newCones);CHKERRQ(ierr);
ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-cones_view", &flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(comm, "Serial Cone Section:\n");CHKERRQ(ierr);
ierr = PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Parallel Cone Section:\n");CHKERRQ(ierr);
ierr = PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscSFView(coneSF, NULL);CHKERRQ(ierr);
}
ierr = DMPlexGetConeOrientations(dm, &cones);CHKERRQ(ierr);
ierr = DMPlexGetConeOrientations(*dmParallel, &newCones);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSFDestroy(&coneSF);CHKERRQ(ierr);
ierr = PetscLogEventEnd(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr);
/* Create supports and stratify sieve */
{
PetscInt pStart, pEnd;
ierr = PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr);
ierr = PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);CHKERRQ(ierr);
}
ierr = DMPlexSymmetrize(*dmParallel);CHKERRQ(ierr);
ierr = DMPlexStratify(*dmParallel);CHKERRQ(ierr);
/* Distribute Coordinates */
{
PetscSection originalCoordSection, newCoordSection;
Vec originalCoordinates, newCoordinates;
const char *name;
ierr = DMGetCoordinateSection(dm, &originalCoordSection);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(*dmParallel, &newCoordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &originalCoordinates);CHKERRQ(ierr);
ierr = VecCreate(comm, &newCoordinates);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) originalCoordinates, &name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) newCoordinates, name);CHKERRQ(ierr);
ierr = DMPlexDistributeField(dm, pointSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(*dmParallel, newCoordinates);CHKERRQ(ierr);
ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr);
}
/* Distribute labels */
ierr = PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr);
{
DMLabel next = mesh->labels, newNext = pmesh->labels;
PetscInt numLabels = 0, l;
/* Bcast number of labels */
while (next) {++numLabels; next = next->next;}
ierr = MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
next = mesh->labels;
for (l = 0; l < numLabels; ++l) {
DMLabel labelNew;
PetscBool isdepth;
/* Skip "depth" because it is recreated */
if (!rank) {ierr = PetscStrcmp(next->name, "depth", &isdepth);CHKERRQ(ierr);}
ierr = MPI_Bcast(&isdepth, 1, MPIU_BOOL, 0, comm);CHKERRQ(ierr);
if (isdepth) {if (!rank) next = next->next; continue;}
ierr = DMLabelDistribute(next, partSection, part, renumbering, &labelNew);CHKERRQ(ierr);
/* Insert into list */
if (newNext) newNext->next = labelNew;
else pmesh->labels = labelNew;
newNext = labelNew;
if (!rank) next = next->next;
}
}
ierr = PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr);
/* Setup hybrid structure */
{
const PetscInt *gpoints;
PetscInt depth, n, d;
for (d = 0; d <= dim; ++d) {pmesh->hybridPointMax[d] = mesh->hybridPointMax[d];}
ierr = MPI_Bcast(pmesh->hybridPointMax, dim+1, MPIU_INT, 0, comm);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetSize(renumbering, &n);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetIndices(renumbering, &gpoints);CHKERRQ(ierr);
ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
for (d = 0; d <= dim; ++d) {
PetscInt pmax = pmesh->hybridPointMax[d], newmax = 0, pEnd, stratum[2], p;
if (pmax < 0) continue;
ierr = DMPlexGetDepthStratum(dm, d > depth ? depth : d, &stratum[0], &stratum[1]);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(*dmParallel, d, NULL, &pEnd);CHKERRQ(ierr);
ierr = MPI_Bcast(stratum, 2, MPIU_INT, 0, comm);CHKERRQ(ierr);
for (p = 0; p < n; ++p) {
const PetscInt point = gpoints[p];
if ((point >= stratum[0]) && (point < stratum[1]) && (point >= pmax)) ++newmax;
}
if (newmax > 0) pmesh->hybridPointMax[d] = pEnd - newmax;
else pmesh->hybridPointMax[d] = -1;
}
ierr = ISLocalToGlobalMappingRestoreIndices(renumbering, &gpoints);CHKERRQ(ierr);
}
/* Cleanup Partition */
ierr = ISLocalToGlobalMappingDestroy(&renumbering);CHKERRQ(ierr);
ierr = PetscSFDestroy(&partSF);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&partSection);CHKERRQ(ierr);
ierr = ISDestroy(&part);CHKERRQ(ierr);
/* Create point SF for parallel mesh */
ierr = PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr);
{
const PetscInt *leaves;
PetscSFNode *remotePoints, *rowners, *lowners;
PetscInt numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints;
PetscInt pStart, pEnd;
ierr = DMPlexGetChart(*dmParallel, &pStart, &pEnd);CHKERRQ(ierr);
ierr = PetscSFGetGraph(pointSF, &numRoots, &numLeaves, &leaves, NULL);CHKERRQ(ierr);
ierr = PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);CHKERRQ(ierr);
for (p=0; p<numRoots; p++) {
rowners[p].rank = -1;
rowners[p].index = -1;
}
if (origCellPart) {
/* Make sure points in the original partition are not assigned to other procs */
const PetscInt *origPoints;
ierr = DMPlexCreatePartitionClosure(dm, origCellPartSection, origCellPart, &origPartSection, &origPart);CHKERRQ(ierr);
ierr = ISGetIndices(origPart, &origPoints);CHKERRQ(ierr);
for (p = 0; p < numProcs; ++p) {
PetscInt dof, off, d;
ierr = PetscSectionGetDof(origPartSection, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(origPartSection, p, &off);CHKERRQ(ierr);
for (d = off; d < off+dof; ++d) {
rowners[origPoints[d]].rank = p;
}
}
ierr = ISRestoreIndices(origPart, &origPoints);CHKERRQ(ierr);
ierr = ISDestroy(&origPart);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&origPartSection);CHKERRQ(ierr);
}
ierr = ISDestroy(&origCellPart);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&origCellPartSection);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
for (p = 0; p < numLeaves; ++p) {
if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */
lowners[p].rank = rank;
lowners[p].index = leaves ? leaves[p] : p;
} else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */
lowners[p].rank = -2;
lowners[p].index = -2;
}
}
for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */
rowners[p].rank = -3;
rowners[p].index = -3;
}
ierr = PetscSFReduceBegin(pointSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr);
ierr = PetscSFReduceEnd(pointSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
for (p = 0; p < numLeaves; ++p) {
if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed");
if (lowners[p].rank != rank) ++numGhostPoints;
}
ierr = PetscMalloc1(numGhostPoints, &ghostPoints);CHKERRQ(ierr);
ierr = PetscMalloc1(numGhostPoints, &remotePoints);CHKERRQ(ierr);
for (p = 0, gp = 0; p < numLeaves; ++p) {
if (lowners[p].rank != rank) {
ghostPoints[gp] = leaves ? leaves[p] : p;
remotePoints[gp].rank = lowners[p].rank;
remotePoints[gp].index = lowners[p].index;
++gp;
}
}
ierr = PetscFree2(rowners,lowners);CHKERRQ(ierr);
ierr = PetscSFSetGraph((*dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr);
ierr = PetscSFSetFromOptions((*dmParallel)->sf);CHKERRQ(ierr);
}
pmesh->useCone = mesh->useCone;
pmesh->useClosure = mesh->useClosure;
ierr = PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr);
/* Cleanup */
if (sf) {*sf = pointSF;}
else {ierr = PetscSFDestroy(&pointSF);CHKERRQ(ierr);}
ierr = DMSetFromOptions(*dmParallel);CHKERRQ(ierr);
ierr = PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
MPI_Comm comm;
DM dm;
Vec v, nv, rv, coord;
PetscBool test_read = PETSC_FALSE, verbose = PETSC_FALSE, flg;
PetscViewer hdf5Viewer;
PetscInt dim = 2;
PetscInt numFields = 1;
PetscInt numBC = 0;
PetscInt numComp[1] = {2};
PetscInt numDof[3] = {2, 0, 0};
PetscInt bcFields[1] = {0};
IS bcPoints[1] = {NULL};
PetscSection section;
PetscReal norm;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, (char *) 0, help);if (ierr) return ierr;
comm = PETSC_COMM_WORLD;
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,"","Test Options","none");CHKERRQ(ierr);
ierr = PetscOptionsBool("-test_read","Test reading from the HDF5 file","",PETSC_FALSE,&test_read,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-verbose","print the Vecs","",PETSC_FALSE,&verbose,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim","the dimension of the problem","",2,&dim,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
ierr = DMPlexCreateBoxMesh(comm, dim, dim == 2 ? 2 : 1, PETSC_TRUE, &dm);CHKERRQ(ierr);
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
numDof[0] = dim;
ierr = DMPlexCreateSection(dm, dim, numFields, numComp, numDof, numBC, bcFields, bcPoints, NULL, NULL, §ion);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dm, section);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr);
ierr = DMSetUseNatural(dm, PETSC_TRUE);CHKERRQ(ierr);
{
DM dmDist;
ierr = DMPlexDistribute(dm, 0, NULL, &dmDist);CHKERRQ(ierr);
if (dmDist) {
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = dmDist;
}
}
ierr = DMCreateGlobalVector(dm, &v);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) v, "V");CHKERRQ(ierr);
ierr = DMGetCoordinates(dm, &coord);CHKERRQ(ierr);
ierr = VecCopy(coord, v);CHKERRQ(ierr);
if (verbose) {
PetscInt size, bs;
ierr = VecGetSize(v, &size);CHKERRQ(ierr);
ierr = VecGetBlockSize(v, &bs);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "==== original V in global ordering. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr);
ierr = VecView(v, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = DMCreateGlobalVector(dm, &nv);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) nv, "NV");CHKERRQ(ierr);
ierr = DMPlexGlobalToNaturalBegin(dm, v, nv);CHKERRQ(ierr);
ierr = DMPlexGlobalToNaturalEnd(dm, v, nv);CHKERRQ(ierr);
if (verbose) {
PetscInt size, bs;
ierr = VecGetSize(nv, &size);CHKERRQ(ierr);
ierr = VecGetBlockSize(nv, &bs);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "==== V in natural ordering. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr);
ierr = VecView(nv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecViewFromOptions(v, NULL, "-global_vec_view");CHKERRQ(ierr);
if (test_read) {
ierr = DMCreateGlobalVector(dm, &rv);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) rv, "V");CHKERRQ(ierr);
/* Test native read */
ierr = PetscViewerHDF5Open(comm, "V.h5", FILE_MODE_READ, &hdf5Viewer);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(hdf5Viewer, PETSC_VIEWER_NATIVE);CHKERRQ(ierr);
ierr = VecLoad(rv, hdf5Viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(hdf5Viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&hdf5Viewer);CHKERRQ(ierr);
if (verbose) {
PetscInt size, bs;
ierr = VecGetSize(rv, &size);CHKERRQ(ierr);
ierr = VecGetBlockSize(rv, &bs);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "==== Vector from file. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr);
ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecEqual(rv, v, &flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "V and RV are equal\n");CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD, "V and RV are not equal\n\n");CHKERRQ(ierr);
ierr = VecAXPY(rv, -1.0, v);CHKERRQ(ierr);
ierr = VecNorm(rv, NORM_INFINITY, &norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "diff norm is = %g\n", (double) norm);CHKERRQ(ierr);
ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Test raw read */
ierr = PetscViewerHDF5Open(comm, "V.h5", FILE_MODE_READ, &hdf5Viewer);CHKERRQ(ierr);
ierr = VecLoad(rv, hdf5Viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&hdf5Viewer);CHKERRQ(ierr);
if (verbose) {
PetscInt size, bs;
ierr = VecGetSize(rv, &size);CHKERRQ(ierr);
ierr = VecGetBlockSize(rv, &bs);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "==== Vector from file. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr);
ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecEqual(rv, nv, &flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "NV and RV are equal\n");CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD, "NV and RV are not equal\n\n");CHKERRQ(ierr);
ierr = VecAXPY(rv, -1.0, v);CHKERRQ(ierr);
ierr = VecNorm(rv, NORM_INFINITY, &norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "diff norm is = %g\n", (double) norm);CHKERRQ(ierr);
ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecDestroy(&rv);CHKERRQ(ierr);
}
ierr = VecDestroy(&nv);CHKERRQ(ierr);
ierr = VecDestroy(&v);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
